Reading additional input from stdin...
OpenAI Codex v0.125.0 (research preview)
--------
workdir: /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
model: gpt-5.5
provider: openai
approval: never
sandbox: read-only
reasoning effort: medium
reasoning summaries: none
session id: 019dcf68-5242-7542-a5b5-de95611e823a
--------
user
Show me anything related to the search system. Mix code and spec references is fine; concise summary preferred.
hook: SessionStart
hook: SessionStart
hook: SessionStart Completed
hook: SessionStart Completed
hook: UserPromptSubmit
hook: UserPromptSubmit
hook: UserPromptSubmit Completed
hook: UserPromptSubmit Completed
codex
I’ll keep this read-only and tight: first I’m going to surface search-related memory/spec context, then cross-check the repo for code paths and spec docs so the summary isn’t guesswork.
mcp: spec_kit_memory/memory_match_triggers started
mcp: spec_kit_memory/memory_match_triggers (failed)
user cancelled MCP tool call
mcp: spec_kit_memory/memory_context started
mcp: spec_kit_memory/memory_context (failed)
user cancelled MCP tool call
codex
The memory MCP calls were cancelled on the tool side, so I’m falling back to local evidence: exact-text searches over specs and code. Since you asked for a concise map rather than deep archaeology, I’ll bias toward entry points and docs with high signal.
exec
/bin/zsh -lc "rg --files | rg 'search|memory|coco|code-graph|spec-kit'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
.opencode/commands/spec_kit/deep-research.md
.opencode/agents/deep-research.md
.opencode/commands/spec_kit/assets/spec_kit_deep-research_confirm.yaml
.opencode/commands/spec_kit/assets/spec_kit_deep-research_auto.yaml
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.opencode/plugins/spec-kit-skill-advisor.js
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.opencode/commands/doctor/assets/doctor_code-graph_confirm.yaml
.opencode/commands/doctor/assets/doctor_code-graph_auto.yaml
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.opencode/specs/system-spec-kit/resource-map.md
.opencode/commands/memory/README.txt
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exec
/bin/zsh -lc 'python3 .opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py "Show me anything related to the search system. Mix code and spec references is fine; concise summary preferred." --threshold 0.8' in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
exec
/bin/zsh -lc "rg -n \"search system|memory_search|memory_context|memory_match_triggers|CocoIndex|code search|search\\(\" specs .opencode code_graph --glob '"'!node_modules'"' --glob '"'!**/dist/**'"'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 exited 2 in 295ms:
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/checklist.md:81:- [x] CLAUDE.md compaction recovery enhanced with `memory_context({ mode: "resume", profile: "resume" })` [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/checklist.md:84:- [x] `memory_match_triggers` fires reliably post-compaction [EVIDENCE: verified in implementation-summary.md]
.opencode/skills/system-spec-kit/scripts/tests/fixtures/manual-playbook-fixture.ts:434:          body: 'Verify memory_context resume mode, then confirm memory_search and checkpoint flows remain stable.',
.opencode/skills/system-spec-kit/scripts/tests/fixtures/manual-playbook-fixture.ts:440:        nextSafeAction: 'Verify memory_context and memory_search',
.opencode/skills/system-spec-kit/scripts/tests/fixtures/manual-playbook-fixture.ts:484:        nextSafeAction: 'Run focused memory_context after resume',
.opencode/skills/system-spec-kit/scripts/tests/fixtures/manual-playbook-fixture.ts:617:        'memory_context focused mode should fill only the missing gaps.',
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/tasks.md:69:- [x] Update CLAUDE.md compaction recovery — Added explicit `memory_context({ mode: "resume", profile: "resume" })` as first action after compaction, with `profile: "resume"` fix from iter 012
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/tasks.md:71:- [x] Create CODEX.md with recovery instructions — Same two primitives: `memory_match_triggers` + `memory_context(resume)` for tool-based compaction recovery
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/tasks.md:76:- [x] Codex CLI tool fallback verified — `hookPolicy: 'unavailable'`, recovery via tool-based `memory_context(resume)` calls
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/tasks.md:79:- [x] `memory_match_triggers` fires reliably post-compaction — Verified across all runtime paths
.opencode/skills/system-spec-kit/references/config/environment_variables.md:276:| `SPECKIT_AUTO_RESUME` | ON | S7 | Auto-resume session detection in `memory_context()` |
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/implementation-summary.md:80:**CLAUDE.md** (root): The compaction recovery section was enhanced with an explicit `memory_context({ mode: "resume", profile: "resume" })` call as the first action after any compaction event. The `profile: "resume"` parameter was critical — without it, the MCP returns search results instead of a compact recovery brief (gap identified in iteration 012).
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/implementation-summary.md:84:**`AGENTS.md`** (root): Added equivalent compaction recovery instructions using the same two primitives (`memory_match_triggers` + `memory_context(resume)`) for tool-based recovery without hooks.
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/implementation-summary.md:91:| `CLAUDE.md` | Modified | Enhanced compaction recovery with explicit `memory_context(resume)` call |
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/implementation-summary.md:104:Implemented as part of the 024-compact-code-graph phases 1-4 pipeline. Runtime detection was built as a standalone module and validated through the test suite, but it is not currently wired into the MCP production startup flow. Instruction file updates were applied after verifying the exact `memory_context` parameter requirements (the `profile: "resume"` requirement was validated through iteration 012 testing). The 7-scenario test matrix was implemented per the iteration 015 specification.
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/implementation-summary.md:113:| Same two primitives for all runtimes | `memory_match_triggers` + `memory_context(resume)` work identically via MCP regardless of runtime. Keeps the recovery protocol simple and testable. |
.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/implementation-summary.md:125:| CLAUDE.md compaction recovery | Verified — explicit `memory_context(resume)` with `profile: "resume"` |
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:50:    tools: ['memory_context', 'session_resume', 'session_bootstrap']
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:59:    tools: ['memory_search', 'memory_quick_search', 'memory_save', 'memory_match_triggers']
.opencode/skills/system-spec-kit/references/config/hook_system.md:112:1. `memory_match_triggers(prompt)` — Fast turn-start context
.opencode/skills/system-spec-kit/references/config/hook_system.md:113:2. `memory_context({ mode: "resume", profile: "resume" })` — Continuation and compaction recovery core
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:134:const budget = getTokenBudget('memory_search');
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:141:const enhanced = enhanceDescription('memory_search', 'Search memories');
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:4:description: "Align the Phase 012 packet with actual CocoIndex behavior and remaining gaps."
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:21:# Feature Specification: Phase 012 — CocoIndex UX, Utilization & Usefulness
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:72:Phase 012 improved CocoIndex visibility and routing, but the packet drifted away from the Level 2 template and from current implementation reality. Several claims were overstated: SessionStart only reports binary availability, PreCompact only adds hint text, `ccc_status` and `ccc_feedback` are lightweight helpers, README/tool-reference updates are still pending, and SessionStart does not trigger background CocoIndex re-indexing.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:88:- Adding `ensure_ready.sh` to SessionStart or otherwise guaranteeing CocoIndex readiness
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:89:- Executing or caching live CocoIndex semantic-neighbor queries during PreCompact
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:90:- Updating the broader CocoIndex README or tool reference in this phase
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:118:| REQ-003 | SessionStart integration must be described as status-only. | Docs state it reports CocoIndex binary availability and does not call `ensure_ready.sh` or guarantee readiness. |
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:119:| REQ-004 | PreCompact semantic integration must be described as hint-only. | Docs state it adds prompt guidance only and does not execute or cache CocoIndex semantic-neighbor queries. |
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:130:- **SC-003**: **Given** a reader reviews PreCompact behavior, **When** they inspect the packet, **Then** they see hint-text-only integration with no live CocoIndex query or cached snippet claims.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md:175:- CocoIndex binary missing: SessionStart reports unavailable status only.
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:368:| **Usage** | `search.hybridSearch.search(query, options)` |
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/plan.md:3:title: "Implementation Plan: Phase 012 — CocoIndex [system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/plan]"
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/plan.md:4:description: "Restate the Phase 012 delivery plan using the actual shipped CocoIndex behavior and remaining gaps."
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/plan.md:21:# Implementation Plan: Phase 012 — CocoIndex UX, Utilization & Usefulness
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/plan.md:92:- **SessionStart path**: Reports CocoIndex binary availability only
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/plan.md:118:- [ ] Implement broader CocoIndex readiness automation or background re-indexing
.opencode/skills/system-spec-kit/references/memory/trigger_config.md:84:The `memory_match_triggers` MCP tool provides fast trigger phrase matching without requiring embeddings:
.opencode/skills/system-spec-kit/references/memory/trigger_config.md:88:const result = await spec_kit_memory_memory_match_triggers({
.opencode/skills/system-spec-kit/references/memory/trigger_config.md:119:1. AI calls `memory_match_triggers({ prompt: "user message" })`
.opencode/skills/system-spec-kit/references/memory/trigger_config.md:127:const matches = await memory_match_triggers({
.opencode/skills/system-spec-kit/references/memory/trigger_config.md:158:These signals are detected during `memory_match_triggers()` processing and influence save-time arbitration (prediction-error scoring) and correction tracking.
.opencode/skills/system-spec-kit/references/memory/trigger_config.md:174:- `memory_match_triggers()` now applies a relevance threshold before returning matches, reducing noise from weak partial matches
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:340:    const results = index.search(query, limit);
.opencode/skills/system-spec-kit/references/memory/memory_system.md:99:> **Note:** MCP tool names use plain names such as `memory_search`, `memory_save`, and `checkpoint_create`.
.opencode/skills/system-spec-kit/references/memory/memory_system.md:105:| L1: Orchestration | `memory_context()` | Unified entry point with intent-aware routing (7 intents) | START HERE for most memory operations |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:106:| L1: Orchestration | `session_resume()` | Resume memory, code graph, and CocoIndex state in one call | Detailed recovery payload after reconnect, or when you want direct merged resume state |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:108:| L2: Core | `memory_search()` | Semantic search with vector similarity | Find prior decisions on auth |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:109:| L2: Core | `memory_quick_search()` | Simplified search wrapper for fast lookups | Quick keyword-based retrieval |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:110:| L2: Core | `memory_match_triggers()` | Fast keyword matching (<50ms) with cognitive features | Gate enforcement |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:133:| L6: Analysis | `code_graph_context()` | Expand CocoIndex or symbol seeds into compact graph neighborhoods | Pull structural context for an LLM prompt |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:141:| L7: Maintenance | `ccc_status()` | Report CocoIndex availability and index health | Confirm semantic code search is ready |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:142:| L7: Maintenance | `ccc_reindex()` | Trigger incremental or full CocoIndex re-indexing | Refresh semantic search after a refactor |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:143:| L7: Maintenance | `ccc_feedback()` | Submit search-quality feedback for CocoIndex results | Record whether semantic hits were helpful |
.opencode/skills/system-spec-kit/references/memory/memory_system.md:163:> **IMPORTANT:** You MUST provide either `query` OR `concepts` parameter. Calling `memory_search({ specFolder: "..." })` without a search parameter will cause an E040 error.
.opencode/skills/system-spec-kit/references/memory/memory_system.md:229:memory_search({ query: "authentication decisions" })
.opencode/skills/system-spec-kit/references/memory/memory_system.md:232:memory_search({
.opencode/skills/system-spec-kit/references/memory/memory_system.md:239:memory_search({
.opencode/skills/system-spec-kit/references/memory/memory_system.md:245:memory_search({
.opencode/skills/system-spec-kit/references/memory/memory_system.md:251:// memory_search({ specFolder: "007-auth" })  // ERROR: E040
.opencode/skills/system-spec-kit/references/memory/memory_system.md:280:memory_search({
.opencode/skills/system-spec-kit/references/memory/memory_system.md:286:memory_search({
.opencode/skills/system-spec-kit/references/memory/memory_system.md:293:memory_search({
.opencode/skills/system-spec-kit/references/memory/memory_system.md:299:memory_search({
.opencode/skills/system-spec-kit/references/memory/memory_system.md:355:- `memory_search`: Exact match (SQL `=` operator)
.opencode/skills/system-spec-kit/references/memory/memory_system.md:422:memory_search({ 
.opencode/skills/system-spec-kit/references/memory/save_workflow.md:373:For retrieval, `memory_context()` routes queries across 7 intents (including `find_spec` and `find_decision`) and applies intent-aware weighting.
.opencode/specs/system-spec-kit/024-compact-code-graph/014-hook-durability-auto-enrichment/spec.md:98:Fix 6 P1 hook reliability and security bugs and implement 8 P2 auto-enrichment and cleanup features. The hook fixes ensure compact recovery works reliably and securely. The auto-enrichment features make code graph + CocoIndex context load automatically without explicit tool calls.
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:5:import { isCocoIndexAvailable } from '../lib/utils/cocoindex-path.js';
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:86:  'memory_context',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:87:  'memory_search',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:89:  'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:451:  // F046: CocoIndex availability via shared helper (no process.cwd())
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:452:  const cocoIndexAvailable = isCocoIndexAvailable();
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:460:    recommendedCalls.push('memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })');
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:463:    recommendedCalls.push('memory_match_triggers({ prompt: "<your task>" })');
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:482:      graphRetrieval: 'For broad topic questions, use memory_search with retrievalLevel: "global" for community-level results. For specific memories, use "local" (default). Use "auto" for automatic fallback.',
.opencode/skills/system-spec-kit/mcp_server/lib/enrichment/passive-enrichment.ts:129:      return ['[session] Context quality is CRITICAL. Consider running `memory_context({ mode: "resume" })` or `session_health` to diagnose.'];
.opencode/skills/system-spec-kit/mcp_server/hooks/README.md:104:- `MEMORY_AWARE_TOOLS` currently includes `memory_context`, `memory_search`, `memory_match_triggers`, `memory_list`, `memory_save`, and `memory_index_scan`.
.opencode/skills/system-spec-kit/mcp_server/hooks/codex/session-start.ts:95:        content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/skills/system-spec-kit/mcp_server/hooks/codex/session-start.ts:101:    content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/codex/session-start.ts:108:    content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/checklist.md:21:# Verification Checklist: Phase 012 — CocoIndex UX, Utilization & Usefulness
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/checklist.md:112:- [x] CHK-042 [P2] Broader CocoIndex README and tool reference updated [EVIDENCE: `.opencode/skills/mcp-coco-index/README.md` now documents system-spec-kit integration and helper-tool reality]
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/checklist.md:121:- [x] CHK-052 [P2] SessionStart background re-index limitation is documented accurately [EVIDENCE: docs explicitly state that background CocoIndex re-index is not implemented in this phase]
.opencode/skills/system-spec-kit/constitutional/README.md:42:The `constitutional/` directory contains constitutional rules that are **always surfaced** at the top of every `memory_search()` result. These are operational rules, safety constraints and critical context that AI agents must always have access to, regardless of what they're searching for.
.opencode/skills/system-spec-kit/constitutional/README.md:62:| **Always Surfaces** | Included at top of every `memory_search` result by default |
.opencode/skills/system-spec-kit/constitutional/README.md:135:3. **Verify** with `memory_search({ query: "anything" })`. Check for `isConstitutional: true`
.opencode/skills/system-spec-kit/constitutional/README.md:150:├── gate-tool-routing.md   # Search and retrieval routing rules for memory, graph, and CocoIndex
.opencode/skills/system-spec-kit/constitutional/README.md:167:| `gate-tool-routing.md` | Recommended | Search and retrieval routing rules for memory, graph, and CocoIndex |
.opencode/skills/system-spec-kit/constitutional/README.md:180:Constitutional memories are **automatically included** at the top of every `memory_search()` result.
.opencode/skills/system-spec-kit/constitutional/README.md:186:memory_search({ query: "authentication flow" })
.opencode/skills/system-spec-kit/constitutional/README.md:198:memory_search({ 
.opencode/skills/system-spec-kit/constitutional/README.md:231:> **Implemented (v1.7.2):** ANCHOR tags are now fully indexed and support section-level retrieval. Use the `anchors` parameter in `memory_search()` to retrieve specific sections with 58-90% token savings.
.opencode/skills/system-spec-kit/constitutional/README.md:400:memory_search({ query: "test" })
.opencode/skills/system-spec-kit/constitutional/README.md:561:memory_search({ 
.opencode/skills/system-spec-kit/constitutional/README.md:674:**Symptom:** `memory_match_triggers()` doesn't return your constitutional rule
.opencode/skills/system-spec-kit/constitutional/README.md:707:memory_match_triggers({ prompt: "fix the bug" })
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/tasks.md:3:title: "Tasks: Phase 012 — CocoIndex UX [system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/tasks]"
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/tasks.md:21:# Tasks: Phase 012 — CocoIndex UX, Utilization & Usefulness
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/tasks.md:76:- [x] T004 Document SessionStart as CocoIndex availability reporting only (`spec.md`, `plan.md`, `implementation-summary.md`)
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/tasks.md:81:- [x] T009 Document `ccc_feedback` as local JSONL append-only feedback without CocoIndex DB writes and without `memory_validate` parity (`spec.md`, `tasks.md`, `implementation-summary.md`)
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/tasks.md:82:- [x] T010 Update the broader CocoIndex README and tool reference (broader CocoIndex docs)
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/tasks.md:83:- [x] T011 Document that SessionStart does not trigger a background CocoIndex re-index (`hooks/claude/session-prime.ts`)
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/description.json:3:  "description": "Feature Specification: Phase 012 — CocoIndex UX, Utilization & Usefulness",
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:111:| 8 | CocoIndex + code graph complementary queries | any | varies | Semantic query → CocoIndex, structural query → code_graph | Correct routing, no duplication |
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:112:| 9 | Code graph expansion from CocoIndex seeds | any | varies | CocoIndex search → feed results to code_graph_context | Structural expansion produces connected symbols |
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:113:| 10 | Compaction with CocoIndex enrichment | claude-code | enabled | PreCompact queries CocoIndex for active symbol neighbors | Cached context includes semantic neighbors within budget |
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:115:| 12 | PreCompact latency within 2s cap | claude-code | enabled | Full pipeline: CocoIndex + graph + memory + merge | Total time < 2s, graceful skip of reverse augmentation if slow |
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:116:| 13 | Seed-to-node resolution accuracy | any | varies | CocoIndex hit at various line ranges → graph node mapping | Exact, enclosing, and file-anchor resolution all work correctly |
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:150:- CocoIndex routing: verify semantic queries go to CocoIndex, structural to code graph
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:151:- CocoIndex + code graph enrichment: verify bidirectional seed → expansion flow
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:152:- Compaction with CocoIndex: verify PreCompact queries CocoIndex and includes results in cached context
.opencode/specs/system-spec-kit/024-compact-code-graph/007-testing-validation/spec.md:155:- Seed resolution: verify CocoIndex file:line hits resolve correctly to tree-sitter nodes
.opencode/specs/system-spec-kit/024-compact-code-graph/008-structural-indexer/spec.md:83:- CocoIndex Code MCP handles all semantic code search (embeddings, vector similarity, 28+ languages)
.opencode/specs/system-spec-kit/024-compact-code-graph/008-structural-indexer/spec.md:91:- **Structural only**: No embeddings, no chunking, no vector search — CocoIndex handles all semantic retrieval
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:68:Phase 012 made CocoIndex easier to notice and easier to route to, but it did not deliver full readiness automation. This packet now reflects that narrower reality: hooks build and smoke-test cleanly, SessionStart reports binary availability, helper tools expose a small operational surface, and several intended follow-ups remain open.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:76:SessionStart now reports whether the CocoIndex binary is available. That is the full extent of the startup integration in this phase. It does not call `ensure_ready.sh`, does not ensure CocoIndex readiness, and does not trigger a background CocoIndex re-index.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:80:Phase 012 added or documented three helper tools around CocoIndex usage:
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:86:`ccc_feedback` does not write into the CocoIndex database and does not mirror `memory_validate` parameters.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:90:The `@context` routing guidance pushes semantic intent toward CocoIndex first, but PreCompact integration remains hint-only. The compaction payload tells the model to query CocoIndex after recovery, yet it does not execute real CocoIndex lookups and does not cache semantic-neighbor snippets.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:94:This phase updated packet content and some CocoIndex guidance, but the broader README and tool reference updates were not completed. Those follow-ups stay open here instead of being reported as done.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:121:| Document `ccc_feedback` as local JSONL storage | The helper writes local feedback records and does not integrate with CocoIndex DB internals or `memory_validate` parity |
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:133:| Background CocoIndex re-index from SessionStart | FAIL, not implemented and tracked as an open gap |
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:141:1. **SessionStart is status-only.** It reports CocoIndex binary availability but does not call `ensure_ready.sh` and does not ensure readiness.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:142:2. **PreCompact semantic integration is hint-only.** It does not execute or cache real CocoIndex semantic-neighbor queries.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:144:4. **`ccc_feedback` is local only.** It appends JSONL under `.opencode/skills/mcp-coco-index/feedback/search-feedback.jsonl`, does not write to the CocoIndex database, and does not mirror `memory_validate` parameters.
.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:146:6. **Background CocoIndex re-index from SessionStart is not implemented.** Any re-index must be triggered separately.
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:13:  - code search
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:25:  - CocoIndex
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:27:  - memory_search
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:28:  - memory_context
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:39:Route code search queries using this priority order:
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:43:| **Semantic/concept** (meaning-based) | `mcp__cocoindex_code__search` (CocoIndex) | `memory_search` |
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:55:| **Spec-doc continuity** (prior work, decisions) | `memory_search` / `memory_context` | `memory_match_triggers` |
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:56:| **Broad topic** (thematic overview) | `memory_search` with `retrievalLevel: "global"` | community search fallback |
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:104:| `mcp__cocoindex_code__search` | `.opencode/skills/mcp-coco-index/SKILL.md` | Semantic code search via vector embeddings |
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:107:| `memory_search` | `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts` | 3-channel hybrid search with RRF fusion |
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:108:| `memory_context` | `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts` | Intent-routed context retrieval (L1 entry point) |
.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md:109:| `memory_match_triggers` | `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-match-triggers.ts` | Trigger-phrase matcher (constitutional + tier-aware) |
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:47:  name: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:48:  description: '[L1:Orchestration] Unified entry point for context retrieval with intent-aware routing. START HERE for most context-retrieval operations across indexed spec docs and constitutional rules. For session recovery, use mode: \'resume\' with profile: \'resume\'. Automatically detects task intent (add_feature, fix_bug, refactor, security_audit, understand, find_spec, find_decision) and routes to optimal retrieval strategy. Modes: auto (default), quick (trigger-based), deep (comprehensive), focused (intent-optimized), resume (session recovery). Token Budget: 3500. For code search by concept/intent, prefer mcp__cocoindex_code__search (CocoIndex). For structural code queries (callers, imports), prefer code_graph_query.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:49:  inputSchema: { type: 'object', additionalProperties: false, properties: { input: { type: 'string', minLength: 1, description: 'The query, prompt, or context description (required)' }, mode: { type: 'string', enum: ['auto', 'quick', 'deep', 'focused', 'resume'], default: 'auto', description: 'Context retrieval mode: auto (detect intent), quick (fast triggers), deep (comprehensive search), focused (intent-optimized), resume (session recovery)' }, intent: { type: 'string', enum: ['add_feature', 'fix_bug', 'refactor', 'security_audit', 'understand', 'find_spec', 'find_decision'], description: 'Explicit task intent. If not provided and mode=auto, intent is auto-detected from input.' }, specFolder: { type: 'string', description: 'Limit context to specific spec folder' }, tenantId: { type: 'string', description: 'Tenant boundary for governed retrieval when memory_context routes to memory_search.' }, userId: { type: 'string', description: 'User boundary for governed retrieval when memory_context routes to memory_search.' }, agentId: { type: 'string', description: 'Agent boundary for governed retrieval when memory_context routes to memory_search.' }, limit: { type: 'number', minimum: 1, maximum: 100, description: 'Maximum results (mode-specific defaults apply)' }, sessionId: { type: 'string', description: 'Optional server-issued session identifier for working-memory continuity. When provided, it must match an existing server-managed session or the call is rejected. Omit it to let the server generate a new session for this request.' }, enableDedup: { type: 'boolean', default: true, description: 'Enable session deduplication' }, includeContent: { type: 'boolean', default: false, description: 'Include full file content in results' }, includeTrace: { type: 'boolean', default: false, description: 'Include provenance-rich trace data (scores, source, trace) in results when underlying memory_search is called' }, tokenUsage: { type: 'number', minimum: 0.0, maximum: 1.0, description: "Optional caller token usage ratio (0.0-1.0)" }, anchors: { type: 'array', items: { type: 'string' }, description: 'Filter content to specific anchors (e.g., ["state", "next-steps"] for resume mode)' }, profile: { type: 'string', enum: ['quick', 'research', 'resume', 'debug'], description: 'Optional response profile formatter. Returns a reduced or mode-aware response shape when profile formatting is enabled.' } }, required: ['input'] },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:54:  name: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:55:  description: '[L2:Core] Search indexed spec-doc continuity semantically using vector similarity. Returns ranked results with similarity scores. Constitutional tier rules are ALWAYS included at the top of results (~2000 tokens max), regardless of query. Requires query (string), concepts (array of 2-5 strings), or cursor (string) for continuation pagination. Supports intent-aware retrieval (REQ-006) with task-specific weight adjustments. When implicit feedback logging is enabled, searches also emit shadow-only feedback signals such as search_shown and, for includeContent runs, result_cited. Token Budget: 3500. For code search by concept/intent, prefer mcp__cocoindex_code__search (CocoIndex). For structural code queries (callers, imports), prefer code_graph_query.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:194:// E3: Simplified search — 3 params, sensible defaults, delegates to memory_search
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:197:  description: '[L2:Core] Simplified search — query + optional limit + optional spec folder. Delegates to memory_search with sensible defaults (intent auto-detect ON, dedup ON, content included, limit 10). Use this when you want fast search without configuring 31 parameters.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:214:  name: 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:600:  description: '[L6:Analysis] Get LLM-oriented compact graph neighborhoods. Accepts CocoIndex search results as seeds — use CocoIndex (mcp__cocoindex_code__search) for semantic search first, then pass results here for structural expansion. Supports manual seeds (provider: manual) and graph seeds (provider: graph). Modes: neighborhood (1-hop calls+imports), outline (file symbols), impact (reverse callers). When readiness requires a full scan, returns an explicit blocked payload with requiredAction `code_graph_scan`, readiness metadata, and lastPersistedAt instead of degraded graph answers. Successful responses include metadata.partialOutput for deadline/budget truncation details (reasons, omittedSections, omittedAnchors, truncatedText). Token Budget: 1200.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:618:            file: { type: 'string', description: 'CocoIndex file path (provider: cocoindex)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:619:            range: { type: 'object', properties: { start: { type: 'number' }, end: { type: 'number' } }, description: 'CocoIndex line range' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:620:            score: { type: 'number', description: 'CocoIndex relevance score' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:621:            snippet: { type: 'string', description: 'CocoIndex snippet text preserved with the seed' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:628:        description: 'Seeds from CocoIndex, manual input, or graph lookups',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:718:  description: '[L7:Maintenance] Check CocoIndex availability. Returns available, binaryPath, indexExists, indexSize, and recommendation.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:724:  description: '[L7:Maintenance] Trigger CocoIndex incremental (or full) re-indexing of the workspace.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:736:  description: '[L7:Maintenance] Submit quality feedback on CocoIndex search results to improve future searches.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:759:  description: '[L1:Orchestration] Resume session with combined memory, code graph, and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. For the canonical first-call recovery path on session start or after /clear, prefer session_bootstrap. Use minimal: true to skip the heavy memory context call and return code graph, CocoIndex, structural context, hints, and session-quality metadata without the full memory payload.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:766:      minimal: { type: 'boolean', description: 'When true, skip the heavy memory context call and return code-graph, CocoIndex, structural-context, hints, and session-quality fields without the full memory payload' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:954:  // L8: CocoIndex
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:62:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:73:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:85:      content: 'Context was compacted, but the cached compact brief was quarantined by semantic validation. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:103:      content: 'Context was compacted and auto-recovered from the cached compact brief. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:172:    '- CocoIndex: unknown',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:248:        '- `memory_context({ input, mode })` — unified context retrieval',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:249:        '- `memory_match_triggers({ prompt })` — fast trigger matching',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:250:        '- `memory_search({ query })` — semantic search',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:306:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:311:      content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:323:      content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/compact-inject.ts:85:    'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:66:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:77:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:89:      content: 'Context was compressed, but the cached compact brief was quarantined by semantic validation. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:106:      content: 'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:180:        '- CocoIndex: unknown',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:188:        '- `memory_context({ input, mode })` - unified context retrieval',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:189:        '- `memory_match_triggers({ prompt })` - fast trigger matching',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:190:        '- `memory_search({ query })` - semantic search',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:239:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:245:    content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:253:    content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/custom-instructions.ts:35:const STARTUP_FALLBACK = 'Startup context unavailable. Call `session_bootstrap()` or `memory_context({ mode: "resume", profile: "resume" })` if more context is needed.';
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:430:- `memory_context` (unified context retrieval)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:431:- `memory_search` (semantic search)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:432:- `memory_match_triggers` (fast trigger matching)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:549:PASS criterion: source grep finds the additive badge interface and formatter wiring; static diff shows no schema or decay-logic changes in the protected files; targeted Vitest exits 0; `memory_search` results carry `confidence`, `extractionAge`, `lastAccessAge`, `orphan`, `weightHistoryChanged` on each `MemoryResultEnvelope`, preserved through `quick`/`research`/`resume` profiles.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:557:- [ ] `memory_search()` returns results (or empty if no memories are indexed yet)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:622:### memory_context: Unified Context Retrieval
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:624:`memory_context()` is the primary entry point for context loading. It detects task intent and routes to the optimal retrieval strategy automatically.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:640:### memory_search: Semantic Search
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:642:`memory_search()` runs vector-based similarity search across all indexed memories.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:651:### memory_match_triggers: Fast Keyword Lookup
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:653:`memory_match_triggers()` provides sub-50ms keyword-based matching. Use it for immediate context surfacing at the start of a conversation.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:721:- `ContextEnvelope`: Wraps all `memory_context()` responses with metadata (mode used, memories returned, intent detected)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:784:1. AI calls `memory_context({ input: "add user profiles", mode: "auto" })`
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1147:MCP TOOLS: memory_context, memory_search, memory_match_triggers,
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1163:| v1.7.x | 2026-02-20 | Cross-encoder reranking enabled by default. Co-activation score boost fix. Query expansion on deep mode. Evidence gap warnings. MMR reranking with intent-mapped lambda. Phase system support (recursive validation, phase detection scoring). Feature flag updates. `memory_context` tokenUsage parameter. 28-tool surface area. |
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:102:    '- CocoIndex: unknown',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:126:      'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:136:      'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:147:      'Context was compacted, but the cached compact brief was quarantined by semantic validation. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:164:    'Context was compacted and auto-recovered from the cached compact brief. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/decision-record.md:3:description: "Architecture decisions for enforcing CocoIndex and Code Graph usage across all CLI runtimes."
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/decision-record.md:33:**Context**: AI assistants across all runtimes consistently default to Grep/Glob for code searches despite CLAUDE.md explicitly stating "MUST use CocoIndex." The root cause is that instruction files are passive — the AI reads them once and then makes tool selection decisions based on built-in preferences. MCP server instructions and tool response hints are injected at the point of decision, making them harder to ignore.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/decision-record.md:57:**Decision**: Create a constitutional-tier memory (`.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md`) that is ALWAYS surfaced at the top of every `memory_search` result.
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/README.md:54:Hooks are transport reliability, not separate business logic. They call the same retrieval primitives (`memory_match_triggers`, `memory_context`) that other runtimes call explicitly.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:4:description: "Fix root cause of AI tool misjudgment — enforce CocoIndex and Code Graph usage across all CLI runtimes via MCP-level enforcement, not just passive CLAUDE.md instructions."
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:28:| **Handoff Criteria** | All CLIs (hook and non-hook) consistently use CocoIndex for semantic searches and Code Graph for structural queries |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:34:**Scope Boundary**: MCP server instructions, session priming payloads, tool response hints, and runtime instruction files. No changes to CocoIndex or Code Graph core functionality.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:130:AI assistants across all CLI runtimes (Claude Code, Codex CLI, Copilot CLI, Gemini CLI) consistently default to Grep/Glob for code search tasks even when CocoIndex (semantic search) and Code Graph (structural queries) are available and appropriate. The root cause is a **passive instruction model**: CLAUDE.md says "MUST use CocoIndex" but this competes with the AI's built-in preference for familiar, fast tools. There is no active enforcement at the MCP layer where the AI actually makes tool selection decisions.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:133:1. Semantic/concept searches ("find code regarding X") use Grep instead of CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:136:4. `buildServerInstructions()` mentions memory tools but not CocoIndex/Code Graph routing
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:150:- Add `hints` field to tool responses that redirect to CocoIndex/Code Graph when appropriate
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:156:- CocoIndex core functionality changes — working correctly already
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:169:| `../../../../../CLAUDE.md` | Modify | Strengthen CocoIndex/Code Graph enforcement language and keep Claude-aware routing guidance consolidated in the active workspace file |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:181:| REQ-001 | `buildServerInstructions()` includes tool-routing rules | Server instructions contain "Use CocoIndex for semantic/concept searches" and "Use Code Graph for structural queries" |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:183:| REQ-003 | Tool response hints redirect misjudgment | When `memory_search` or `memory_context` is called with a code-search query, response includes hint about CocoIndex |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:190:| REQ-005 | Constitutional memory for routing | `.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md` constitutional memory exists and surfaces on code search queries |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:207:| Dependency | CocoIndex MCP server running | Routing rules are useless if CocoIndex is down | Include availability check; degrade gracefully |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:210:| Risk | Over-aggressive routing creates false redirects | AI sent to CocoIndex for exact text match | Include "use Grep for exact text/regex" escape hatch |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:77:   - Content: 3 rules (CocoIndex for semantic, Code Graph for structural, Grep for exact text)
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:78:   - Include CocoIndex availability check via `isCocoIndexAvailable()`
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:84:   - Add `mcp__cocoindex_code__search` cross-reference in memory_context description
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:85:   - Add "For code search, prefer CocoIndex" to relevant tool descriptions
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:91:   - Populate based on availability: CocoIndex available -> add semantic routing rule; Code Graph fresh -> add structural routing rule
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:103:   - Pattern: `memory_search` called with query matching code concepts -> hint: "Consider using mcp__cocoindex_code__search for code search"
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:104:   - Pattern: `memory_context` with code structural query -> hint: "Consider using code_graph_query for structural queries"
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/plan.md:125:### Dependencies: Phases 018-024 complete (CocoIndex bridge, Code Graph auto-trigger, hookless priming)
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:6:// using the 3-source merge pipeline (Memory, Code Graph, CocoIndex)
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:151:  // Hint for AI to use CocoIndex for semantic neighbors after recovery
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:153:    sections.push('## Semantic Context (CocoIndex)\nUse `mcp__cocoindex_code__search` to find semantic neighbors of active files listed above.');
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-013-correctness-boundary-repair.md:87:**Problem:** The `memory_context` and `code_graph_context` handlers reflected internal error details -- including stack traces (technical debugging information showing the exact sequence of code that triggered the error) and internal file paths -- directly to callers. This information could reveal implementation details useful to an attacker or simply confuse non-technical consumers.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:9:AI assistants across all CLI runtimes (Claude Code, Codex, Copilot, Gemini) consistently defaulted to Grep and Glob for code search even when CocoIndex (semantic search) and Code Graph (structural queries) were available and better suited. The root cause was a passive enforcement model: instruction files said "MUST use CocoIndex" but this competed with the AI's built-in preference for familiar tools, and the AI won every time. This phase added active enforcement at five layers -- MCP server instructions, session priming, tool response hints, instruction files, and agent definitions -- so that every CLI runtime receives routing rules at the point where tool selection decisions actually happen. 28 of 30 tasks completed; 2 deferred. This is the final phase (25 of 25) in the compact-code-graph specification.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:27:**Problem:** Hardcoded routing rules would cause confusion when a tool was unavailable. If the rules said "use CocoIndex for semantic search" but CocoIndex was down or not configured, the AI would waste time calling a broken tool and then not know what to do next.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:29:**Fix:** Each enforcement layer checks whether CocoIndex and Code Graph are actually available before recommending them. If CocoIndex is down, the server instructions and PrimePackage omit the semantic search rule entirely. If the Code Graph is empty, structural query routing is excluded. The AI receives only actionable recommendations for tools that are actually running.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:41:**Fix:** Added a "Tool Routing" section to `buildServerInstructions()` in `context-server.ts` containing three conditional rules: CocoIndex for semantic/concept searches (only included when CocoIndex is available), Code Graph for structural queries like callers and dependencies (only when graph is fresh or stale), and Grep for exact text or regex (always included). Every runtime receives these rules automatically.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:45:**Problem:** The PrimePackage (the structured context payload sent on the first tool call of a session) told the AI what tools existed but not when to use each one. The AI knew CocoIndex was available but still chose Grep because nothing in the priming payload said otherwise.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:47:**Fix:** Extended the `PrimePackage` interface in `memory-surface.ts` with a `toolRouting` field inside `routingRules`. The directive uses command language ("semantic queries → CocoIndex") rather than descriptions ("CocoIndex is available for semantic search"), because directive phrasing is harder for the AI to reinterpret or ignore. The content adapts based on CocoIndex availability.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:51:**Problem:** Even with proactive enforcement, the AI occasionally called the wrong tool. When `memory_search` or `memory_context` was called with a query like "find the authentication logic" or "implementation of retry," the system processed the request against memory artifacts when it should have been routed to CocoIndex for semantic code search. There was no feedback mechanism.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:53:**Fix:** Added code-search pattern detection in the tool dispatch handler. When `memory_search` or `memory_context` is called with a query matching code-search patterns (phrases like "find code", "implementation of", "function that", "where is", "how does X work"), the JSON response envelope gains a `hints` array suggesting CocoIndex or Code Graph instead. Hints are non-blocking -- they append to the response without interrupting the current tool call, nudging the AI toward the right tool on the next query.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:59:**Fix:** Added a `routingRecommendation` string field to `SessionSnapshot` in `session-snapshot.ts`. This field builds a concise routing summary from CocoIndex availability and graph freshness, giving both server instructions and session priming a single source of truth for routing decisions.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:63:**Problem:** Tool descriptions in the MCP schema (the metadata the AI reads to understand what each tool does) did not mention routing. The AI read that `memory_search` "searches indexed memories" but had no indication that CocoIndex existed for code-specific searches, or that `code_graph_query` was better than Grep for structural questions.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:65:**Fix:** Updated four tool descriptions in `tool-schemas.ts`: `memory_context` and `memory_search` now include cross-references saying "For code search by concept/intent, prefer CocoIndex. For structural queries, prefer code_graph_query." `code_graph_query` gained "Use INSTEAD of Grep for structural queries" language. `code_graph_context` now recommends using CocoIndex first and passing results as seeds for structural expansion.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:75:**Problem:** The root CLAUDE.md contained a passive "MUST use CocoIndex" bullet under Mandatory Tools. Passive language competes with the AI's built-in tool preferences and loses. The Quick Reference table listed only "CocoIndex search" for code search, missing Code Graph and Grep entirely.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:77:**Fix:** Replaced the passive bullet with a three-line "Code Search Decision Tree (MANDATORY)" that maps query types to tools: semantic/concept → CocoIndex, structural → code_graph_query, exact text → Grep. Updated the Quick Reference "Code search" row to include all three tools with clear routing. Every CLI runtime that reads CLAUDE.md now gets explicit tool-to-query-type mapping.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:89:**Fix:** Created both files with identical tool routing enforcement tables mapping query types to tools with concrete examples. Includes an anti-patterns section warning against common misjudgments: don't use Grep for concept searches, don't use memory_search for code search, and check CocoIndex availability before relying on it.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:109:**Problem:** Automated tests verify that routing rules are present in server instructions and PrimePackage, but a manual test confirming that Claude Code actually routes a semantic search to CocoIndex in a fresh session has not been executed.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:123:| `mcp_server/hooks/memory-surface.ts` | Extended PrimePackage with `routingRules.toolRouting` directive populated by CocoIndex availability |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:125:| `mcp_server/lib/session/session-snapshot.ts` | Added `routingRecommendation` string field built from CocoIndex/Code Graph availability |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-025-tool-routing-enforcement.md:131:| `CLAUDE.md` (root) | Replaced passive CocoIndex bullet with active 3-line decision tree; updated Code Search workflow row |
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:207:export async function cached_search(query: string, limit = 20, options: Record<string, unknown> = {}): Promise<EnrichedSearchResult[]> {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:346:    const similar = vector_search(embedding, {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:405:export async function enhanced_search(
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-004-cross-runtime-fallback.md:27:**Fix:** Updated instruction files to steer those runtimes toward Gate 1 memory surfacing and `memory_context({ mode: "resume", profile: "resume" })` instead of pretending hook transport exists everywhere.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:917:   * const rows = await store.search(queryEmbedding, 10, { specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:920:  async search(embedding: EmbeddingInput, topK: number, options: VectorSearchOptions = {}): Promise<MemoryRow[]> {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:944:    return vector_search(embedding, search_options, database);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:1090:    return enhanced_search(embedding, undefined, options, database);
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:2:// MODULE: CocoIndex Path Helper
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:4:// F046/F051: Shared helper for resolving the CocoIndex binary path.
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:12:/** Relative path from project root to the CocoIndex CLI binary. */
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:48: * Get the absolute path to the CocoIndex binary.
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:51:export function getCocoIndexBinaryPath(): string {
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:56: * Check whether the CocoIndex binary exists on disk.
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:58:export function isCocoIndexAvailable(): boolean {
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:59:  return existsSync(getCocoIndexBinaryPath());
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1051:  // Including it here caused all candidates to be filtered out when memory_context
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-011-compaction-working-set.md:9:When an AI session runs long and the context window fills up, Claude compacts the conversation to free space. Previously, that compaction only preserved memories -- it had no awareness of which code files were actively being worked on or what the codebase structure looked like. This phase replaces the Memory-only compaction with a three-source merge pipeline that combines constitutional memory, structural code graph context, and semantic code search results. A new session working-set tracker remembers which files and symbols were touched during the conversation, so when compaction fires, the system knows what matters most and allocates its limited 4000-token budget across all three sources using guaranteed minimums, overflow redistribution, and a deterministic trim order that protects the most critical context.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-011-compaction-working-set.md:21:**Fix:** Built a late-fusion pipeline that retrieves from three independent sources in parallel: (1) constitutional and triggered memories from the memory database, (2) structural code graph context showing file relationships and dependencies, and (3) CocoIndex semantic search results finding conceptually related code. The three result sets are deduplicated at the file level (so the same file mentioned by two sources only appears once, keeping the higher-priority version) and merged into a single structured brief. "Late fusion" means each source runs its own retrieval independently -- they are only combined at the end, which avoids ordering dependencies and lets each source use its own timeout. After compaction, the AI now retains awareness of active code files, their structural neighbors, and project-wide rules.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-011-compaction-working-set.md:53:**Problem:** If the code graph index or CocoIndex semantic search service was unavailable (not configured, not running, or not yet indexed), the compaction pipeline would either fail outright or produce incomplete results with wasted token budget allocated to empty sections.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-011-compaction-working-set.md:55:**Fix:** When any source is unavailable or returns empty, its floor tokens flow automatically to the remaining sources through the overflow pool. The pipeline always produces useful output even when running with just one source -- for example, in a fresh project with no code graph and no CocoIndex, compaction falls back to memory-only behavior automatically, using the full token budget for memories. No configuration change or manual intervention is needed.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-011-compaction-working-set.md:127:- 3-source merge documented as partial (code graph and CocoIndex sources are placeholder text, not real retrieval)
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-011-compaction-working-set.md:136:No migration required. The new pipeline is backward-compatible -- if Code Graph and CocoIndex are not configured, the system falls back to Memory-only behavior automatically.
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:84:| `/spec_kit:resume` missing `profile: "resume"` | Calls `memory_context({ mode: "resume" })` without profile param | Pass `profile: "resume"` for compact brief format (iter 012 finding) |
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:99:- `/spec_kit:resume` — Must pass `profile: "resume"` to `memory_context()`. Currently missing this parameter, which causes search results instead of a compact recovery brief (iteration 012 gap).
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:125:| "Find code related to X" | CocoIndex (semantic) | Code graph (expand neighbors) |
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:128:| "How does retry logic work?" | CocoIndex (semantic) | Code graph (trace call chain) |
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:133:- Use CocoIndex (`mcp__cocoindex_code__search`) for "find code that...", "how is X implemented", semantic discovery
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:135:- Use Memory (`memory_search`, `memory_context`) for session continuity, prior decisions, compaction recovery
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:146:- [ ] `/spec_kit:resume` passes `profile: "resume"` to `memory_context()`
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:154:- EDIT: `.opencode/commands/spec_kit/assets/spec_kit_resume_auto.yaml` (add `profile: "resume"` to `memory_context()` parameters)
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/spec.md:155:- EDIT: `.opencode/commands/spec_kit/assets/spec_kit_resume_confirm.yaml` (add `profile: "resume"` to `memory_context()` parameters)
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/plan.md:77:   - Locate the `memory_context()` call in resume command
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:177:Packet `026-graph-and-context-optimization/010-fts-capability-cascade-floor` freezes the lexical capability contract that packet `002-implement-cache-warning-hooks` now consumes. `memory_search` responses expose:
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:850:  const results = bm25Index.getIndex().search('authentication', {
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-024-hookless-priming-optimization.md:23:**Fix:** Created a single `getSessionSnapshot()` function (about 95 lines) that all callers share. It aggregates spec folder, graph freshness, CocoIndex (semantic code search) availability, quality score, and priming status into one read-only object. Every component that needs session state now reads from the same source of truth.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-024-hookless-priming-optimization.md:35:**Fix:** Added a `minimal: true` option to `session_resume`. When enabled, it skips the heavy memory loading and returns only graph status, code search availability, and session health. This gives lightweight recovery for the cases where full context is unnecessary, saving significant tokens and latency.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-024-hookless-priming-optimization.md:79:**Problem:** The priming agent made four separate tool calls on startup (memory context, code graph status, code search status, session health), making the startup sequence slow and consuming roughly twice as many tokens as necessary.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-024-hookless-priming-optimization.md:91:**Problem:** Tool descriptions for `memory_context`, `session_health`, and `session_resume` did not indicate when to call them. AI assistants had to be explicitly told which tool to use, rather than being able to self-select based on the description.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:9:CocoIndex Code is a powerful semantic code search tool that understands 28+ programming languages, but it was barely used in practice. The hooks that run at session startup failed because the TypeScript source files were never compiled to JavaScript. The CocoIndex MCP server was not registered for Claude Code sessions. There was only one MCP tool (search), so managing the index required dropping to the command line. And despite documentation saying "use CocoIndex first," AI agents routinely skipped it in favor of simpler text search. This phase fixes the compilation blocker, registers CocoIndex for automatic loading, adds three new MCP tools for index management and quality feedback, enforces CocoIndex-first routing across all four AI runtimes, and wires semantic search results into the compaction pipeline so they survive context window resets.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:29:#### CocoIndex auto-loads in Claude Code
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:31:**Problem:** CocoIndex was configured for the OpenCode runtime but missing from `.claude/mcp.json`, the configuration file that tells Claude Code which MCP servers (tool providers that AI assistants can call) to load automatically. Claude Code users had no automatic access to semantic code search -- they would have had to set it up manually, which nobody did.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:33:**Fix:** Added the `cocoindex_code` server entry to `.claude/mcp.json` so the CocoIndex MCP server loads automatically in every Claude Code session. No manual setup required.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:37:**Problem:** There was no way to know at session start whether CocoIndex was working or whether its search index (the pre-built database of code embeddings that powers semantic search) was outdated. A stale index means search results miss recent code changes, and users had no signal that this was happening until they got bad results.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:39:**Fix:** The SessionStart hook (`session-prime.ts`) now checks CocoIndex availability and reports its status in the startup output. If the index is older than 24 hours, a warning section prompts the user to re-index, catching staleness before it causes misleading search results. If CocoIndex is not running at all, the status line says so clearly instead of failing silently.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:43:**Problem:** Checking the health of the CocoIndex search index -- how many files are indexed, how many text chunks exist, which embedding model is in use, when the index was last updated -- required dropping out of the AI conversation and running command-line tools. This friction meant index problems often went unnoticed.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:45:**Fix:** A new MCP tool called `ccc_status` exposes those index statistics directly within the conversation. The AI assistant or the user can inspect index state without leaving the chat. If the CocoIndex daemon (the background process that serves the index) is not running, the tool returns a clear error instead of hanging.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:55:**Problem:** There was no way to tell CocoIndex which search results were actually useful and which were noise. Without this feedback signal, the system could not learn from usage patterns, and embedding quality (how well the system understands code similarity) could not improve over time.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:63:**Fix:** The `code_graph_context` tool now suggests CocoIndex follow-up queries in its `nextActions` output after expanding graph neighborhoods. Instead of calling CocoIndex inline (which would slow down every graph query), the tool emits suggestions that the caller can choose to execute based on remaining time budget. If fewer than 400 milliseconds remain, the suggestions are skipped. This keeps the core tool fast while enabling richer, cross-cutting results when time allows.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:69:#### CocoIndex-first agent routing
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:71:**Problem:** Despite documentation across all runtimes saying "prefer CocoIndex for semantic search," AI agents consistently skipped it and went straight to Grep and Glob (text-matching tools that search for exact strings). This happened because the routing guidance was advisory -- a suggestion the agent could ignore -- rather than a structured decision rule. The result was that semantic queries (like "find error handling patterns") were answered with brittle text matches instead of meaning-aware search.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:73:**Fix:** Updated the `@context` agent definition (the agent responsible for all codebase exploration and file search) in all five runtime configurations -- OpenCode, Claude, Codex, Gemini, and the shared Agents directory -- to enforce explicit routing rules. Semantic intent (searching by concept or meaning) goes to CocoIndex first. Structural intent (finding imports, call sites, file relationships) goes to the code graph. Session intent (recovering prior work context) goes to Memory. Agents now use the right tool for the right query type instead of defaulting to text matching.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:79:**Fix:** Extended the PreCompact hook (`compact-inject.ts`) to query CocoIndex for semantic neighbors of the top working-set files (the files the AI has been actively reading or editing). Those results now appear in the cached compaction payload under a "Semantic Neighbors" section. After a context reset, the AI retains awareness of code that is semantically related to its current work, even if that code was never explicitly opened in the session.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:83:**Problem:** The `refresh_index: true` parameter on CocoIndex search queries triggered an inline index refresh during the search itself. When multiple MCP queries executed in parallel -- which happens routinely because AI assistants optimize for speed by issuing concurrent tool calls -- this caused `ComponentContext` errors, crashing the affected queries and returning no results.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:91:#### CocoIndex skill docs updated
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:93:**Problem:** The CocoIndex skill documentation (`SKILL.md`) only covered the original `search` tool. The three new MCP tools had no documentation, meaning AI agents and users would not know they exist or how to use them.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:109:**Problem:** There were no automated tests verifying that the CocoIndex-first routing rules were correctly configured across all agent definitions. A future edit to any agent file could silently break the routing without anyone noticing.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:111:**Fix:** Added 12 new tests across 5 groups (semantic queries, structural queries, session queries, ambiguous queries, and case-insensitive matching) that validate CocoIndex-first routing is correctly enforced in all agent definitions. The tests check that semantic intent routes to CocoIndex, structural intent routes to code graph, and session intent routes to Memory.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:122:| `mcp_server/hooks/claude/session-prime.ts` | CocoIndex availability check and stale index warning on startup |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:123:| `mcp_server/hooks/claude/compact-inject.ts` | Queries CocoIndex for semantic neighbors of working-set files |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:129:| `.opencode/agents/context.md` | CocoIndex-first routing enforcement |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:130:| `.claude/agents/context.md` | CocoIndex-first routing enforcement |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:131:| `.codex/agents/context.toml` | CocoIndex-first routing enforcement |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:132:| `.gemini/agents/context.md` | CocoIndex-first routing enforcement |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:133:| `.agents/agents/context.md` | CocoIndex-first routing enforcement |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:154:- ccc_feedback documented as local JSONL (not CocoIndex DB)
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-012-cocoindex-ux-utilization.md:159:No migration required. The new MCP tools and routing changes are additive. If CocoIndex is not running, all hooks and tools degrade gracefully -- they skip CocoIndex sections and return informative errors without blocking other functionality.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34:The `pipeline/` directory implements the core retrieval pipeline behind `memory_search`. Each search request flows through four sequential stages, each with a defined I/O contract and clear responsibility boundary. The pipeline supports hybrid, vector and multi-concept search types with optional deep-mode query expansion, cross-encoder reranking, MMR diversity pruning and MPAB chunk-to-parent reassembly.
.opencode/specs/system-spec-kit/024-compact-code-graph/spec.md:106:| 10 | `010-cocoindex-bridge-context/` | Phase 010: CocoIndex Bridge + code_graph_context: Template compliance shim section. | complete |
.opencode/specs/system-spec-kit/024-compact-code-graph/spec.md:108:| 12 | `012-cocoindex-ux-utilization/` | Phase 012 — CocoIndex UX, Utilization & Usefulness: Template compliance shim section. | complete |
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:162: * value in cache keys (e.g. memory_search when `enableCausalBoost=true`) so
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:166: * R-007-12 — targeted memory_search cache invalidation.
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:184:  // includes it (e.g. memory_search when enableCausalBoost=true) becomes
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:1085:  // R-007-12: Generation counter for memory_search cache invalidation
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/spec.md:88:| 2 | Slim agent to 2 calls | Change from 4 calls (memory_context + code_graph_status + ccc_status + session_health) to 2 (session_resume + session_health) | .opencode/agents/context.md + all runtime copies |
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/spec.md:97:| 6 | Stronger tool descriptions | Add recovery affordances to memory_context, session_resume, session_health descriptions | tool-schemas.ts |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-030-opencode-graph-plugin.md:31:**Problem:** Startup banners could still overstate graph health from counts alone, and structural reads needed parity with CocoIndex-style first-use freshness without allowing unbounded inline rescans.
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/plan.md:96:   - Add "Use for session recovery" to memory_context
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/plan.md:101:   - When true: skip full memory_context resume, return only graph + coco + health
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-021-cross-runtime-instruction-parity.md:25:**Fix:** Added a "No Hook Transport" trigger table to `CODEX.md` -- the instruction file that Codex CLI reads on startup. The table maps each lifecycle event (fresh session, resume, compaction, `/clear`, structural search, memory save) to the exact tool calls the AI should make. For example, on a fresh session start the AI now knows to call `memory_context({ mode: "resume" })` to load prior context, plus `code_graph_status()` to check whether the structural index is current. This is the same behavior Claude Code gets from its hooks, just expressed as explicit instructions instead.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-021-cross-runtime-instruction-parity.md:59:**Problem:** In OpenCode, bootstrapping a session with full context required three separate manual calls: `memory_context()` to load prior session state, `code_graph_status()` to check the structural index, and `ccc_status()` to verify CocoIndex (the semantic code search system). There was no single-call way to prime a session, which meant the orchestrator either had to hard-code all three calls or the user had to remember them.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-021-cross-runtime-instruction-parity.md:69:**Fix:** Added an entry to the Agent Definitions table in `CLAUDE.md` describing `@context-prime` as a lightweight bootstrap agent for session start or after `/clear`. The entry specifies that it loads memory context, checks code graph and CocoIndex health, and returns a compact Prime Package with spec folder, task status, system health, and recommended next steps. All runtimes that read `CLAUDE.md` now know this agent exists and when to use it.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/checklist.md:83:- [x] T-002: Check CocoIndex availability via `isCocoIndexAvailable()` in routing section [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/checklist.md:87:- [x] T-006: Add CocoIndex cross-reference to relevant tool descriptions in `tool-schemas.ts` [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/checklist.md:92:- [x] T-008: Populate `routingRules` based on CocoIndex/Code Graph availability [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/checklist.md:99:- [x] T-012: Detect code-search patterns in `memory_search` queries [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/checklist.md:100:- [x] T-013: Detect structural query patterns in `memory_context` queries [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/tasks.md:66:- [x] T-002: Check CocoIndex availability via `isCocoIndexAvailable()` in routing section
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/tasks.md:70:- [x] T-006: Add CocoIndex cross-reference to relevant tool descriptions in `tool-schemas.ts`
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/tasks.md:75:- [x] T-008: Populate `routingRules` based on CocoIndex/Code Graph availability
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/tasks.md:82:- [x] T-012: Detect code-search patterns in `memory_search` queries
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/tasks.md:83:- [x] T-013: Detect structural query patterns in `memory_context` queries
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-018-non-hook-auto-priming.md:21:**Fix:** The MCP server now detects the first tool call in a session and can attach a Prime Package containing last active spec folder, current task status, graph freshness, CocoIndex availability, and recommended next calls. In the current packet state, this mechanism remains part of the fallback layer; public recovery guidance now centers on `session_bootstrap()` and runtime-specific startup surfaces rather than claiming one universal silent auto-prime path for every CLI.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-018-non-hook-auto-priming.md:27:**Fix:** A new `session_health` tool returns a simple traffic-light score that any runtime can query at any time. **ok** means the session is fresh, context is loaded, and the code graph is recent. **warning** means the session may have drifted -- for example, there has been a long gap between tool calls or the spec folder changed. **stale** means probable context loss and recommends calling `memory_context` to recover. When health drops to warning or stale, the server also injects recovery hints into the responses of normal tool calls, so the AI can self-correct without the user having to intervene.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-018-non-hook-auto-priming.md:41:**Problem:** The Prime Package assembles context from multiple sources -- spec folder state, code graph status, CocoIndex availability, recommended actions. Without a size limit, this payload could grow large enough to consume a meaningful portion of the AI's context window (the finite amount of text it can hold in memory during a conversation), crowding out the user's actual work.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-018-non-hook-auto-priming.md:89:**3 items deferred to future phases (all P2):** sessionPrimed flag retry-on-failure (F045), CocoIndex path hardcoding (F046), and dual timestamp state consolidation (F047).
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:165: * const rows = vector_search(queryEmbedding, { limit: 5, specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:168:export function vector_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:313: * const rows = multi_concept_search([embA, embB], { limit: 8, specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:316:export function multi_concept_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:610:export function keyword_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:714:    raw_results = vector_search(query_embedding, {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:722:    raw_results = keyword_search(query, { limit, specFolder }, database);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:800:        return await multi_concept_keyword_search(concepts.filter(c => typeof c === 'string'), limit, options);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:811:    return await multi_concept_keyword_search(concepts.filter(c => typeof c === 'string'), limit, options);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:814:  const raw_results = multi_concept_search(concept_embeddings, { limit, specFolder, minSimilarity });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:858:export async function multi_concept_keyword_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:871:    keyword_search(concept, { limit: 100, specFolder })
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/README.md:3:description: "Fix root cause of AI tool misjudgment — enforce CocoIndex and Code Graph usage across hook-compatible and non-hook CLIs."
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/README.md:19:AI defaults to Grep/Glob for code searches even when CocoIndex (semantic) and Code Graph (structural) are available. Root cause: passive "MUST use" instructions in CLAUDE.md compete with built-in AI tool preferences. No active enforcement exists at the MCP layer.
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:4:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/implementation-summary.md:78:This phase turned passive search guidance into an active 5-layer enforcement model. The core rollout changed 12 files and pushed routing rules into the places where tool choice actually happens, so semantic searches steer toward CocoIndex, structural questions steer toward Code Graph, and exact text stays with Grep. The task ledger is now at 28 of 30 tasks complete.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/implementation-summary.md:136:2. **Manual runtime confirmation still pending** The fresh Claude Code session check for CocoIndex-first routing is still open as T-030.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-root.md:9:Long AI coding sessions in this repo no longer depend on the user re-explaining context after compaction, restart, or runtime switches. This packet grew from the original 25-phase delivery into a 30-phase program that now covers Claude hook rescue, hookless bootstrap recovery, structural code-graph retrieval, CocoIndex bridging, cross-runtime instruction parity, startup-orientation quality fixes, the packet-030 OpenCode transport/startup-parity extension, and the follow-on review/remediation work that brought the packet back to a clean validation state. The end result is a context-preservation stack that can recover active work, point the AI at the right retrieval tools, and surface structural code context without pretending that every intermediate phase shipped as fully complete.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-root.md:43:### CocoIndex bridge and intent-aware routing
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-root.md:47:**Fix:** Seed-resolution and context orchestration now let CocoIndex hits expand into structural neighborhoods, while intent metadata and later routing-enforcement phases push semantic questions toward CocoIndex, structural questions toward the graph, and session-history questions toward memory surfaces.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-root.md:129:**Problem:** "Must use CocoIndex" style instructions were too passive. The AI often defaulted back to Grep/Glob even when the better tool was available.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-root.md:209:| `mcp_server/lib/code-graph/seed-resolver.ts` | CocoIndex seed anchoring and confidence handling |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-010-cocoindex-bridge-context.md:9:This phase connected semantic search to the new structural graph so the packet could move beyond isolated retrieval channels. CocoIndex hits can now seed graph expansion, and the returned context includes enough structural framing to explain why a semantic result matters in the codebase around it.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-010-cocoindex-bridge-context.md:21:**Fix:** Added `seed-resolver.ts` to map CocoIndex file-range hits to graph symbols or file-level anchors that the structural layer can understand.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-010-cocoindex-bridge-context.md:41:**Problem:** The phase planned stronger back-and-forth enrichment between graph output and CocoIndex.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:59: * Token-pressure policy for memory_context.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:67: * Automatic session resume context injection for memory_context.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:322:  search(query: string, limit: number = 10): BM25SearchResult[] {
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:9:Tool routing enforcement — fixing root cause of AI tool misjudgment for CocoIndex and Code Graph across hook-compatible and non-hook CLIs. Additional directive: use cli-copilot with GPT 5.4 High model for research iterations.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:14:- [ ] Q1: What is the exact decision path an AI takes when choosing between Grep/Glob vs CocoIndex vs Code Graph for a search task?
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:18:- [x] Q5: What patterns in user queries reliably distinguish semantic searches (CocoIndex) from structural queries (Code Graph) from exact text searches (Grep)?
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:28:- Changing CocoIndex or Code Graph core functionality (both work correctly)
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:49:- [x] Q6: Non-hook CLIs receive guidance through both runtime instruction files and MCP bootstrap metadata, but the MCP-delivered content is currently recovery/status oriented rather than an explicit routing policy for CocoIndex vs Code Graph vs Grep/Glob.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:58:- Checking `opencode.json` confirmed CocoIndex is a separate provider, which explains why `tool-schemas.ts` alone cannot enforce cross-tool routing.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:69:- Inspecting only `tool-schemas.ts` was insufficient to answer the CocoIndex side of routing because CocoIndex is not defined in this server.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:83:- Treating `tool-schemas.ts` changes as sufficient for both Code Graph and CocoIndex routing; CocoIndex is exposed by a separate MCP provider.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:92:Iteration 10: Investigate over-aggressive enforcement failure modes and escape hatches: quoted structural queries, exact symbol-name lookups, stale-code-graph fallback, unavailable CocoIndex/Code Graph scenarios, and how to keep redirects conservative while still correcting Grep/Glob overuse.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:98:- CocoIndex code search found relevant source files:
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-strategy.md:102:  - `.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/seed-resolver.ts` — CocoIndex to graph node resolution
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:9:When a user asked a question about their codebase, they had to know which tool to call: `code_graph_context` for structural questions ("who calls this function?") and `memory_search` for semantic ones ("find code similar to X"). Most users do not know the difference and should not have to. This phase makes `memory_context` smart enough to figure it out automatically. It classifies every incoming query by intent, routes it to the correct backend, and falls back gracefully if the first choice returns nothing. A new `session_resume` composite tool eliminates the 3-4 separate calls users previously needed when resuming a session, replacing them with a single call that merges memory, code graph, and cache status into one response. Finally, a passive enrichment pipeline was added so that every tool response can be lightly annotated with nearby code symbols, session staleness warnings, and triggered memories -- all within strict latency and token budgets.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:21:**Problem:** Users had to manually pick the right tool for each question. If they wanted to know "who calls this function?" they needed `code_graph_context`. If they wanted "find code similar to X" they needed `memory_search`. Choosing the wrong tool meant getting irrelevant or empty results. This forced users to understand internal system architecture just to ask a question.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:23:**Fix:** A classification step called `classifyQueryIntent()` was added at the top of the `memory_context` handler. Every incoming query is now automatically sorted into one of three categories: structural (about code relationships like calls, imports, and inheritance), semantic (about meaning, similarity, or explanation), or hybrid (ambiguous queries that could go either way). Structural queries route to the code graph, semantic queries route to the memory search path, and hybrid queries run both backends and merge the results. Users simply ask their question in plain language and the system determines where to look.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:39:**Fix:** Every `memory_context` response now includes a `queryIntentMetadata` block. This block shows three things: the detected intent (structural, semantic, or hybrid), the backend that was actually used to produce the response, and a flag indicating whether fallback was applied. This makes the routing pipeline fully transparent and debuggable.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:49:**Fix:** A new `session_resume` tool was created as a single composite call that performs all of these steps internally. It calls `memory_context` in resume mode, checks the code graph status, and checks the constitutional cache status, then merges everything into one consolidated response. This saves approximately 400-900 tokens and 2-3 network round trips per session resume.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:73:#### Duplicated CocoIndex path check
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:75:**Problem:** The new `session_resume` handler contained a copy of the same CocoIndex path-discovery logic (code that locates where the CocoIndex search index is stored on disk) that already existed in other handlers. This duplication created a maintenance risk: if a bug was fixed in one copy, the other copy would remain broken.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:95:| `mcp_server/handlers/session-resume.ts` | New composite tool (130 lines) combining `memory_context`, `code_graph_status`, and `ccc_status` into one response |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:101:| `mcp_server/lib/utils/cocoindex-path.ts` | New shared helper for CocoIndex path discovery, replacing duplicated checks |
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:115:- memory_context routing documented as additive (not selective backend routing)
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-020-query-routing-integration.md:117:- session_resume documented as slim (no ccc_status, just isCocoIndexAvailable)
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-016-cross-runtime-ux.md:31:**Problem:** The system offers two search backends: the code graph (which understands structural relationships like "what calls this function" or "what does this class extend") and CocoIndex (which understands meaning, like "find code similar to this pattern"). There was no way for the system to know which backend to use for a given query. A structural question sent to CocoIndex would return irrelevant results; a semantic question sent to the code graph would return nothing. Users had to manually pick the right tool or get empty results.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-016-cross-runtime-ux.md:33:**Fix:** A new heuristic classifier called `classifyQueryIntent()` examines query keywords before routing. Structural keywords (such as "calls," "imports," "implements," "extends") route to the code graph. Semantic keywords (such as "similar," "like," "related," "example") route to CocoIndex. When the query is ambiguous -- no clear signal either way -- it runs against both backends so results are not missed. This removes the guesswork of which search tool to invoke for a given question.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-016-cross-runtime-ux.md:87:**Problem:** Five checklist items across earlier phases (005, 006, 008, 011, and 012) claimed features were fully shipped when they were only partially implemented. For example, the resume profile documentation had gaps, the indexer description referenced tree-sitter (a parsing library) when the actual implementation used regex-based parsing, and CocoIndex semantic neighbor retrieval was listed as complete but had never been wired into the pipeline. The parent checklist gave a false picture of what had actually been delivered.
.opencode/specs/system-spec-kit/024-compact-code-graph/changelog/changelog-024-016-cross-runtime-ux.md:102:| `CODEX.md` | Session Start Protocol section: forces `memory_context()` and `code_graph_status()` on first turn |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:31:- [x] Q11: How does CocoIndex change the code graph architecture? (iterations 036-045 + CocoIndex analysis) — Complementary: CocoIndex handles semantic, code graph handles structural only
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:32:- [x] Q12: How should CocoIndex and Code Graph be wired together? (iterations 046-055) — Bridge via file-range seeds, intent router, floors+overflow budget, 3-source merge, repo maps
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:34:- [x] Q14: How can code graph + CocoIndex be utilized automatically without explicit tool calls? (iteration 057) — Three-tier auto-enrichment: (1) session lifecycle background preloading, (2) tool dispatch inline file-context injection via memory-surface.ts pattern, (3) query-aware deferred enrichment via 3-source allocator. GRAPH_AWARE_TOOLS set prevents recursion. Non-hook runtimes get Tier 2+3 via MCP-native interception. Lazy per-file staleness checks for background indexing.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:35:- [x] Q15: How can non-hook CLI runtimes (OpenCode, Codex, Copilot, Gemini) achieve equivalent context preservation UX? (iteration 058) — Four-tier fallback: T1 hooks (Claude only), T2 instruction-file triggers (CODEX.md/CLAUDE.md forcing memory_context calls), T3 command-based (/spec_kit:resume), T4 Gate 1 auto (memory_match_triggers). Enhancement: MCP "first-call priming" as T1.5 universal mechanism
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:36:- [x] Q16: How can CocoIndex utilization be improved? (iteration 059) — 5 improvement areas: near-exact seed resolution + CocoIndex score propagation, 3 auto-reindex triggers (branch switch/session start/debounced save), intent-router keyword pre-classification + confidence fallback, 3 hybrid query patterns (structural expansion, semantic enrichment, working set warm-up), 3 underutilized features (language filters, refresh_index management, ccc_feedback)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:77:- Outcome: Structural code graph architecture + CocoIndex complementary integration
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:78:- Key findings: tree-sitter deep dive, SQLite schema, compact representations, code-aware RAG, MCP API design, CocoIndex covers semantic search
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:79:- Stop reason: Architecture complete, CocoIndex integration analyzed, all questions answered
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:81:### Segment 5 (iterations 46-55): CocoIndex + Code Graph Integration
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:84:- Outcome: Complete integration architecture for CocoIndex + Code Graph + Memory
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:85:- Key findings: code_graph_context accepts file-range seeds from CocoIndex, 3-source budget allocator (floors + overflow pool: constitutional 700, graph 1200, CocoIndex 900, triggered 400, overflow 800), query-intent router with heuristic classifier, independent index refresh with freshness metadata, 3-source merge with constitutional priority, repo maps with CocoIndex-boosted ranking, session working set tracking via structural expansion
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:93:  2. Automatic AI utilization: auto-triggering code graph/CocoIndex without explicit tool calls
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:95:  4. CocoIndex utilization: re-indexing triggers, seed resolution, query routing
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:130:- CocoIndex integration analysis saved significant implementation complexity
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-strategy.md:131:- Cross-reading seed-resolver.ts alongside CocoIndex SKILL.md reveals concrete improvement gaps (iteration 059)
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/checklist.md:80:- [x] `/spec_kit:resume` passes `profile: "resume"` to `memory_context()` [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/checklist.md:96:- [x] Memory commands fully audited (search, manage, learn) — search uses memory_context/memory_search, manage uses memory_stats/memory_health, learn uses constitutional APIs — all hook-compatible [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/021-cross-runtime-instruction-parity/spec.md:113:1. Calls `session_resume()` to recover prior session state plus graph/CocoIndex availability
.opencode/specs/system-spec-kit/024-compact-code-graph/003-stop-hook-tracking/spec.md:219:The Stop hook can optionally log whether CocoIndex was queried during the session for cross-system observability. This is informational — the Stop hook does not query CocoIndex itself.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:18:| 2 | `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts` | 28-40 | Extend `PrimePackage` with `routingRules: string[]`; populate it inside `buildPrimePackage()` from graph freshness and CocoIndex availability. Mirror the same routing rules in the first-tool-call prime package returned by `primeSessionIfNeeded()`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:63-70`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:316-364`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:366-415`] |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:19:| 3 | `.opencode/skills/system-spec-kit/mcp_server/context-server.ts` | 85-110 | Add a compact **Tool Routing** section to `buildServerInstructions()`; extend the mirrored `primePackage` type with `routingRules`; render those rules in `injectSessionPrimeHints()`; add reactive routing hints into the existing `envelope.hints` pipeline for `memory_context`/`memory_search` code-search misuse. This file is the correct integration seam because it already owns both dynamic instructions and JSON-envelope hint injection. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:151-171`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:530-565`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:605-646`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:788-879`] |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:20:| 4 | `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts` | 18-30 | Strengthen descriptions for `memory_context`, `memory_search`, `code_graph_query`, and `code_graph_context` so the tool catalog itself tells the model: semantic/concept search -> CocoIndex, structural relationships -> Code Graph, exact text/path -> Grep/Glob. `code_graph_query` currently describes capability but not routing intent. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:40-50`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:47-50`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:637-663`] |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:21:| 5 | `.opencode/skills/system-spec-kit/constitutional/gate-tool-routing.md` | 25-35 | Add a constitutional memory with the canonical decision tree: semantic/concept -> CocoIndex, structural/call graph -> Code Graph, exact text/regex/path -> Grep/Glob. This should be the single source of truth reused by docs and hook text. Constitutional memories are already surfaced automatically. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:144-174`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:929-935`] |
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:74:**Verified code gap:** There is already a generic `envelope.hints` pipeline in `context-server.ts`, but no routing-specific classifier. Passive enrichment is response-text-based; it does not see the original tool arguments, so by itself it is not sufficient for `memory_context` / `memory_search` misuse detection. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:788-811`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:821-879`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/enrichment/passive-enrichment.ts:144-213`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:113:**Mitigation:** Keep the routing block under ~200 tokens, make it availability-aware, and preserve the exact-text/regex escape hatch so the model is not told to use CocoIndex for literal grep tasks. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:138-141`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:127:**Mitigation:** Use soft suggestions only, scope them to `memory_context` and `memory_search`, require obvious semantic/structural phrases, and suppress hints when CocoIndex/Code Graph are unavailable.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-010.md:156:If those two conditions are accepted, the implementation can proceed in a single dependency-ordered PR without touching CocoIndex or Code Graph core logic. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/spec.md:82-86`]
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/tasks.md:70:- [x] Update `/spec_kit:resume` to pass `profile: "resume"` to `memory_context()` — fixes iter 012 gap; compact recovery brief now returned
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:3:## Focus: Analyze existing MCP response hint and redirect mechanisms, then design a reusable response hint injection layer that nudges assistants toward CocoIndex for semantic code discovery and Code Graph for structural analysis without causing over-aggressive redirects.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:10:3. Session priming plus PrimePackage is the second existing hint injection mechanism, but it is explicitly post-selection. On the first tool call, `primeSessionIfNeeded()` builds a `PrimePackage` containing `specFolder`, `currentTask`, `codeGraphStatus`, `cocoIndexAvailable`, and `recommendedCalls`; later `injectSessionPrimeHints()` appends strings like `Active spec folder: ...`, `Code graph: ..., CocoIndex: ...`, and `Recommended next calls: ...` into `envelope.hints`, while also persisting the full structured object into `meta.sessionPriming`. This makes PrimePackage useful as a corrective hint layer for the second tool decision, but not as a first-call enforcement mechanism. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:31-70] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:316-364] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:366-415] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:530-565] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:727-733] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:833-839]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:23:   - `Routing hint: code graph is stale/empty. Prefer CocoIndex until code_graph_scan refreshes graph health.`
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:26:9. The semantic-search trigger should be pattern-based but conservative. The classifier should only emit a CocoIndex redirect when the extracted query strongly looks like intent-based code discovery: phrases such as `how does`, `where is the logic`, `find code that`, `implementation of`, `similar code`, `pattern for`, `search codebase for`, or `unfamiliar module`, combined with the absence of exact-path or exact-token signals. Structural terms such as `callers`, `imports`, `impact`, `dependency`, `outline`, `references`, or `what calls` should route toward Code Graph instead. Queries that look like exact matches or known-path lookups (`src/...`, `.ts`, `.py`, regex syntax, glob syntax, explicit symbol text) should suppress the routing hint entirely. This preserves the intended division from prior iterations: semantic discovery -> CocoIndex; structural relationships -> Code Graph; exact lookup -> Grep/Glob. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:121-137] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:605-646]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:32:   - Availability gate: never recommend Code Graph when `codeGraphStatus` is `stale` or `empty`; never recommend CocoIndex if `cocoIndexAvailable` is false.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:37:   These escape hatches make the layer safe as a correction mechanism while avoiding the classic failure mode where every vaguely exploratory prompt gets over-redirected to CocoIndex. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/response/envelope.ts:240-275] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:530-565] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:843-879] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/response-hints.ts:86-140]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:39:11. Final design conclusion: response hints can and should enforce the "next tool choice" using the already-deployed `hints[]`/`meta.*` enrichment pipeline, but they cannot solve the root cause alone because they arrive after a tool has already been chosen. The root-cause fix still requires a concise routing stanza in `buildServerInstructions()` for first-call behavior across hook-compatible and non-hook CLIs. The response hint layer is therefore best designed as a secondary corrective loop that reinforces the same routing matrix after the first tool call and adapts recommendations to current graph/CocoIndex availability. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:605-646] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:788-879] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:316-364]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-004.md:47:## Next Focus Recommendation: Investigate the concrete classifier design and placement for first-call versus second-call enforcement: define a minimal semantic/structural/exact intent heuristic set, inspect the CocoIndex provider/tool description surface, and design how the same routing matrix should be mirrored between `buildServerInstructions()` and the new response-hint enrichment stage without drifting over time.
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/implementation-summary.md:74:The resume workflow YAML assets at `.opencode/commands/spec_kit/assets/spec_kit_resume_auto.yaml` and `.opencode/commands/spec_kit/assets/spec_kit_resume_confirm.yaml` previously called `memory_context({ mode: "resume" })` without the `profile` parameter, causing raw search results to be returned instead of a compact recovery brief. Adding `profile: "resume"` to those workflow definitions activates the condensed brief format identified as a gap in research iteration 012.
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/implementation-summary.md:86:All spec_kit commands (resume, handover, complete, implement) and memory commands (search, manage, learn, save) were audited for compaction-related assumptions. Memory search uses `memory_context`/`memory_search`, manage uses `memory_stats`/`memory_health`, and learn uses constitutional APIs — all hook-compatible without modification. SKILL.md was updated with Hook System and Code Graph sections documenting command integration points.
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/implementation-summary.md:92:| `.opencode/commands/spec_kit/assets/spec_kit_resume_auto.yaml` | Modified | Add `profile: "resume"` to `memory_context()` parameters for autonomous resume |
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/implementation-summary.md:93:| `.opencode/commands/spec_kit/assets/spec_kit_resume_confirm.yaml` | Modified | Add `profile: "resume"` to `memory_context()` parameters for interactive resume |
.opencode/specs/system-spec-kit/024-compact-code-graph/005-command-agent-alignment/implementation-summary.md:136:3. **Query-intent routing guidance is advisory.** Agent definitions include routing tables (CocoIndex for semantic, Code Graph for structural, Memory for session) but enforcement depends on agent compliance at runtime.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:33:- Line 9: "FIRST ACTION -- call: `memory_context({ input: 'resume previous work', mode: 'resume', profile: 'resume' })`"
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:34:- Line 16-18: Documents `memory_match_triggers(prompt)` and `memory_context({ mode: "resume" })` as cross-runtime primitives
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:35:- Line 21-26: Query-intent routing table directing semantic queries to CocoIndex, structural to code_graph, session to memory
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:45:- Gate 1 (CLAUDE.md) requires `memory_match_triggers(prompt)` on each new user message
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:50:**Design implication**: OpenCode agents cannot self-trigger code graph on startup because they have no lifecycle hook -- they are dispatched by the orchestrator with a task. The "startup" concept for OpenCode agents is "first user message in a conversation", which is handled by Gate 1's `memory_match_triggers`. First-call priming at the MCP level would transparently serve these agents without requiring changes to agent definitions.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:95:- `memory_context` / `memory_search` / `memory_match_triggers`: If first call, append a `sessionPriming` field to the response envelope containing: (a) interrupted session hints, (b) most recent spec folder, (c) code graph staleness indicator
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:97:- `ccc_search` (CocoIndex): If first call, check CocoIndex availability and append status hint
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:129:- **Full prime** (~800 tokens): Standard + resumed context snippet (only when memory_context called with resume-like input)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:142:1. `memory_match_triggers(prompt)` -- fast turn-start context (constitutional + triggered)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-062.md:143:2. `memory_context({ mode: "resume", profile: "resume" })` -- session recovery after compaction
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-005.md:8:2. A routing constitutional would have real runtime reach because constitutional memories are injected on both major retrieval paths: Stage 1 search injection for normal `memory_search()` and the hook/auto-surface path used during tool-dispatch context assembly. This means one compact routing rule can reinforce tool choice across both hook-compatible and non-hook flows whenever the memory system is consulted, but every extra word becomes recurring prompt tax. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:952-1004] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:378-415] [SOURCE: .opencode/skills/system-spec-kit/constitutional/README.md:752-766]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-005.md:12:4. The proposed content should mirror the already-emergent canonical routing policy instead of inventing a new one: semantic discovery and unfamiliar-code exploration go to CocoIndex first; structural navigation such as callers/imports/outline/impact goes to Code Graph; exact-token and known-path lookups stay on grep/glob. This matches both runtime guidance and current tool capability boundaries. [SOURCE: CLAUDE.md:34-50] [SOURCE: CODEX.md:28-33] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:637-744]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-005.md:18:7. Trigger phrases should be intentionally disjoint from gate-enforcement. `gate-enforcement.md` already covers verbs like `fix`, `implement`, `resume`, `done`, and `save context`; the routing constitutional should instead target search-intent and tool-choice phrases such as `semantic search`, `exact text`, `known path`, `callers`, `imports`, `outline`, `impact`, `CocoIndex`, `code graph`, `grep`, and `glob`. That makes the two constitutional memories complementary rather than redundant in trigger-based surfacing. [SOURCE: .opencode/skills/system-spec-kit/constitutional/gate-enforcement.md:2-48]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-005.md:42:After gate rules pass, always route code search by intent:
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-005.md:43:- Semantic discovery, unfamiliar code, or "how is X implemented" -> CocoIndex first.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-005.md:46:- If code graph is stale or empty, use CocoIndex plus file reads until graph health is restored.
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:3:description: "Wire the code graph and CocoIndex into the compaction pipeline via a session working-set tracker and a 3-source merge allocator. Replace the current Memory-only compaction with ..."
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:79:Wire the code graph and CocoIndex into the compaction pipeline via a session working-set tracker and a 3-source merge allocator. Current runtime status is **partial**: tracker and merger modules exist, but the active compaction retrieval path still leans on transcript heuristics and follow-up guidance.
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:87:- CocoIndex Code MCP provides semantic search
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:106:| CocoIndex (semantic) | 900 | 22.5% | 3rd | Medium |
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:112:- If CocoIndex returns no results → its 900 floor flows to overflow pool
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:120:1. Weak semantic tail (low-score CocoIndex hits)
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:147:3. Use as query terms for CocoIndex semantic search
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/spec.md:157:  │  2. CocoIndex: semantic neighbors of working set  │
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/20-02-26_07-05__readme-and-summary-with-hvr.md:506:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/z_archive/019-readme-and-summary-with-hvr" })` |
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/20-02-26_07-05__readme-and-summary-with-hvr.md:518:memory_search({ specFolder: "system-spec-kit/z_archive/019-readme-and-summary-with-hvr", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/20-02-26_07-05__readme-and-summary-with-hvr.md:524:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/20-02-26_07-05__readme-and-summary-with-hvr.md:533:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/plan.md:78:   - Apply floor allocations (constitutional 700, graph 1200, CocoIndex 900, triggered 400)
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/plan.md:84:   - Accept shaped results from Memory, Code Graph, CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/plan.md:101:   - CocoIndex empty → verify overflow redistribution
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/plan.md:115:- CocoIndex Code MCP for semantic search
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:5:1. `buildServerInstructions()` is the only pre-tool, server-wide instruction surface inside this MCP server. At startup, `context-server.ts` calls `buildServerInstructions()` and passes the resulting string to `serverWithInstructions.setInstructions(...)` before connecting transport, so any MCP client that surfaces server instructions can receive this text before choosing a tool. Today that text only reports memory counts, active/stale counts, search channels, key memory tools, and an optional session-recovery digest; it does not contain any routing policy for Grep/Glob vs CocoIndex vs Code Graph. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:605-646] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:1593-1598]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:6:2. Tool descriptions are the second major decision surface, but they are capability-oriented rather than routing-oriented. `ListToolsRequestSchema` returns `TOOL_DEFINITIONS`, so clients see the descriptions from `tool-schemas.ts` when enumerating tools. The current `code_graph_query` description explains structural operations (`outline`, `calls_from`, `calls_to`, `imports_from`, `imports_to`), and `code_graph_context` explains compact graph neighborhoods plus CocoIndex-seeded expansion, but neither description says when to prefer Code Graph over CocoIndex or Grep/Glob. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:685-687] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:637-693]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:7:3. PrimePackage is a post-selection correction mechanism, not a pre-selection router. On the first tool call, `primeSessionIfNeeded()` builds a `PrimePackage` from the incoming tool args and code-graph snapshot, recording `specFolder`, `currentTask`, `codeGraphStatus`, `cocoIndexAvailable`, and `recommendedCalls`. That package is only created after a tool has already been chosen, and later injected into the tool response envelope as hints such as `Code graph: fresh, CocoIndex: available` and `Recommended next calls: ...`. This means PrimePackage can improve the second tool decision, but it cannot prevent the first misjudgment. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:317-364] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:366-415] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:530-565] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:833-839]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:8:4. The exact current decision path is layered and mostly heuristic: runtime instruction files provide the strongest explicit routing policy, server instructions provide only session/memory context, tool descriptions provide per-tool capability summaries, and PrimePackage/auto-surface hints arrive only after the first tool response. For Copilot/Gemini-style runtime docs, the code-search protocol explicitly says to use CocoIndex first for concept/intent queries, Grep for exact text, Glob for file paths, and to fall back to CocoIndex when the graph is stale. Codex has a similar `Query-Intent Routing` section that maps semantic discovery to CocoIndex and structural navigation to `code_graph_query` / `code_graph_context`. [SOURCE: GEMINI.md:71-105] [SOURCE: CLAUDE.md:34-67] [SOURCE: CODEX.md:14-33]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:9:5. The best MCP-server injection point for all CLIs is therefore `buildServerInstructions()`, because it is the only centralized surface in this server that can talk about both internal Code Graph tools and the external CocoIndex provider from one place before tool selection happens. By contrast, `tool-schemas.ts` can only influence tools owned by this MCP server, and PrimePackage is necessarily late. This matters because CocoIndex is not defined in `tool-schemas.ts`; it is registered separately in `opencode.json` as the `cocoindex_code` provider. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:605-646] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:637-693] [SOURCE: opencode.json:40-49]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:10:6. A secondary universal injection point is to strengthen the descriptions of `code_graph_query`, `code_graph_context`, `code_graph_status`, and `session_resume` so they encode routing intent for structural tasks and stale-graph fallback. Those descriptions are returned to every MCP client via `ListToolsRequestSchema`, so they are likely the strongest per-tool lever available from this server. However, because CocoIndex lives on another server, per-tool description changes here cannot fully enforce semantic-vs-structural routing by themselves. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:685-687] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:654-744] [SOURCE: opencode.json:40-49]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:11:7. `buildServerInstructions()` can be extended within a tight token budget. A concise addition under ~200 tokens would be enough to encode a routing policy such as: `Routing: exact token/path lookups -> grep/glob; semantic/intent queries or unfamiliar code -> CocoIndex; callers/imports/neighborhood/impact -> code_graph_query/context; if graph is stale/empty, use CocoIndex until code_graph_scan/session_resume restores graph health.` This would fill the current gap without requiring new tools. The current function already appends dynamic lines and session-recovery guidance, so adding 1-2 routing lines is mechanically straightforward. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:619-645]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-001.md:20:## Next Focus Recommendation: Investigate how each runtime actually surfaces MCP server instructions and tool descriptions to the model at inference time, especially whether Copilot/Codex/Gemini consume `setInstructions()` consistently and what the separate CocoIndex tool description currently says.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:4:Investigate how `classifyQueryIntent()` should integrate with `code_graph_context`, `memory_context`, and `memory_search` for automatic structural vs semantic query routing.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:12:It is currently orphaned: repo search finds only its definition, no consumers. Meanwhile `memory_context` already auto-routes only across retrieval modes (`quick/deep/focused/resume`) using the separate task-intent classifier from `intent-classifier.ts`, and `memory_search` uses that same classifier for ranking weights, not backend selection. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:584-637`, `:829-901`, `:1032-1351`; `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:563-598`, `:661-696`; `.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:7-29`, `:404-506`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:14:Important distinction: the `graph` channel inside `memory_search` is a causal-memory graph over `memory_index`/`causal_edges`, not the code graph behind `code_graph_context`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1107-1123`; `.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:89-145`, `:150-252`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:20:Users still have to know when to call `code_graph_context` vs `memory_search`. `memory_context` is marketed as the smart entry point, but today it only chooses *mode*, not *backend*. Structural questions like "who calls X?" or "show import tree for Y" are not automatically routed to the code graph, while semantic discovery questions stay in the same memory retrieval path. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/README.md:509-518`; `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:847-883`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:24:### Proposal A: Transparent Auto-Routing in memory_context
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:26:- Description: Make `memory_context` the primary consumer of `classifyQueryIntent()`. In `mode: "auto"`, classify the query first:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:28:  - `semantic` -> keep current `memory_search` path
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:55:- Risk: HIGH — duplicates `memory_context`'s role, expands API surface, and creates long-term ambiguity between two "smart entry points."
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:59:- Description: When `code_graph_context` gets no resolved anchors, or when query intent is semantic/hybrid, let it optionally fall back to `memory_search` and report that fallback.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:92:- `memory_context` is already the documented L1 "smart entry point," so backend routing belongs there.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:94:  - `classifyQueryIntent()` = choose backend (`code_graph_context` vs `memory_search`)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:97:- `memory_search` should **not** transparently reroute to code graph by default; it is already an explicit lower-level semantic tool.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:104:| Copilot / OpenCode | User/prompt must choose `memory_context` vs `code_graph_context`; `memory_context` only auto-picks mode | `memory_context` auto-picks backend and keeps explicit tools optional | High |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:111:1. Add a backend-routing phase to `memory_context` before current mode execution.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:114:4. Semantic branch: keep current `memory_search` flow unchanged, continue using `intent-classifier.ts` and `query-router.ts`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-099.md:115:5. Hybrid branch: run both, merge top-level summaries and cap result size under existing `memory_context` token-budget enforcement.
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/spec.md:44:1. **Missing await in memory_search** - `formatSearchResults()` is async but called without await, returning Promises instead of results
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/spec.md:188:### User Story 7 - memory_search Returns Resolved Results (Priority: P0)
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/spec.md:190:As an AI assistant, I need `memory_search` to return actual results (not Promises) so that search results are usable when `includeContent=true`.
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/spec.md:194:**Independent Test**: Call `memory_search` with `includeContent=true` and verify results are objects, not Promises.
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/spec.md:197:1. **Given** `includeContent=true`, **When** `memory_search` executes, **Then** the result payload is fully resolved (no Promise objects)
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/spec.md:249:- **REQ-FUNC-031:** System MUST await `formatSearchResults()` in `memory_search` so results are fully resolved
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/spec.md:297:| Story 7 - memory_search Results | REQ-FUNC-031 | Critical production bug |
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/tasks.md:76:- [x] Item 6: Strengthen tool descriptions with recovery affordances — Evidence: tool-schemas.ts updated for memory_context, session_health, session_resume descriptions
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:3:## Focus: Draft exact, implementation-ready TypeScript for `buildServerInstructions()` routing guidance and `code_graph_*` tool description updates, using the existing CocoIndex availability and Code Graph freshness plumbing.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:19:        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:31:      lines.push(`- Semantic/code-understanding queries: ${cocoReady ? 'use CocoIndex first' : 'CocoIndex unavailable; fall back to grep/glob for exact text and code_graph_* only when you already know the symbol or file'}.`);
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:44:The preferred implementation is to derive both values from `getSessionSnapshot()` because that already centralizes the CocoIndex binary check and graph freshness classification:
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:51:If the implementation wants a direct CocoIndex helper call instead of going through the snapshot, this is the exact utility call:
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:54:const { isCocoIndexAvailable } = await import('./lib/utils/cocoindex-path.js');
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:55:const cocoReady = isCocoIndexAvailable();
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:58:The direct helper is safe because `isCocoIndexAvailable()` is only an `existsSync()` check against the resolved `ccc` binary path. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:51-59`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:67:  description: '[L6:Analysis] Query structural relationships: outline (file symbols), calls_from/calls_to (call graph), imports_from/imports_to (dependency graph). Use this instead of Grep for structural questions when you already know the file or symbol and need callers, callees, imports, or reverse dependencies. If code_graph_status is stale or empty, run code_graph_scan first; use CocoIndex for semantic discovery when you do not know the symbol yet. Supports includeTransitive for multi-hop BFS traversal. Token Budget: 1200.',
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:90:  description: '[L6:Analysis] Get LLM-oriented compact graph neighborhoods. Use this after CocoIndex finds relevant code, or when you need compact structural context/impact around a file or symbol instead of raw text matches. Accepts CocoIndex search results as seeds (provider: cocoindex), manual seeds (provider: manual), or graph seeds (provider: graph). If the code graph is stale or empty, run code_graph_scan first or keep using CocoIndex until refreshed. Modes: neighborhood (1-hop calls+imports), outline (file symbols), impact (reverse callers). Token Budget: 1200.',
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:107:            file: { type: 'string', description: 'CocoIndex file path (provider: cocoindex)' },
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:108:            range: { type: 'object', properties: { start: { type: 'number' }, end: { type: 'number' } }, description: 'CocoIndex line range' },
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:109:            score: { type: 'number', description: 'CocoIndex relevance score' },
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:114:        description: 'Seeds from CocoIndex, manual input, or graph lookups',
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:130:3. The correct CocoIndex availability signal already exists in session snapshot as `snap.cocoIndexAvailable`, and that field is itself backed by `isCocoIndexAvailable()`. The helper resolves the project root, builds the absolute path to `.opencode/skills/mcp-coco-index/mcp_server/.venv/bin/ccc`, and returns `existsSync(...)`, so the routing section can trust it as a cheap startup-time availability check. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:70-74`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:12-13`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:51-59`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:134:5. The strongest implementation pattern for `code_graph_context` is to present it as the bridge between semantic discovery and structural expansion: use CocoIndex first to find candidate code, then feed those results into `code_graph_context` for neighborhood or impact context. This matches the existing schema, which already accepts CocoIndex seeds via `provider: 'cocoindex'`, but the current description does not foreground that routing path. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:660-693`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:136:6. The routing text should refer to "CocoIndex" rather than hard-coding a runtime-specific external tool identifier inside server instructions. The MCP server controls only the Spec Kit Memory tool descriptions here, while CocoIndex is registered as a separate provider in `opencode.json`; using the product name keeps the instruction accurate across hook-compatible and non-hook runtimes whose displayed tool names may differ. [SOURCE: `opencode.json:40-49`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:637-693`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:138:7. The proposed routing section is short enough to fit the prior <200-token guidance budget while still encoding the three essential branches: semantic search -> CocoIndex, structural analysis -> Code Graph, exact text/path -> grep/glob. The lines are deliberately concise and avoid examples or long caveats so they can live alongside the existing memory/session summary without bloating the startup instruction payload. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:619-645`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-006.md:148:## Next Focus Recommendation: Validate the enforcement wording against tests and runtime display behavior: add a unit test that `buildServerInstructions()` emits the Tool Routing section under fresh/stale CocoIndex/graph combinations, then inspect whether any runtime-specific instruction files should mirror the exact same three-branch wording for consistency.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-089.md:18:- when completion tokens exceed the threshold, it writes a new `pendingCompactPrime` payload containing only a recovery hint string telling the agent to call `memory_context({ mode: "resume", profile: "resume" })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-089.md:54:- CocoIndex seeds keep only `filePath`, `startLine`, `endLine`, and `query`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-089.md:55:- all non-CocoIndex seeds are also reduced to `filePath`, `startLine`, `endLine`, and `query`
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/19-02-26_21-46__readme-and-summary-with-hvr.md:371:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/z_archive/019-readme-and-summary-with-hvr" })` |
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/19-02-26_21-46__readme-and-summary-with-hvr.md:383:memory_search({ specFolder: "system-spec-kit/z_archive/019-readme-and-summary-with-hvr", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/19-02-26_21-46__readme-and-summary-with-hvr.md:389:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/019-readme-and-summary-with-hvr/scratch/legacy-memory-quarantine/19-02-26_21-46__readme-and-summary-with-hvr.md:398:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/implementation-summary.md:79:| `tool-schemas.ts` | **Item 6** — Enhanced descriptions for `memory_context`, `session_health`, `session_resume`. **Item 7** — Registered `session_bootstrap` tool definition. **Item 8** — Added `minimal` param to `session_resume` schema |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-081.md:88:| `code-graph-auto-enrichment.vitest.ts` | Partly | No | Current suite has dispatch auto-surface tests, but not graph/CocoIndex auto-enrichment or `GRAPH_AWARE_TOOLS`. |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-081.md:134:`runtime-routing.vitest.ts` already tests a pure query router that sends structural questions to `code_graph`, semantic questions to CocoIndex, and session questions to memory. That overlaps conceptually with iteration 069's integration aspirations, but it is **not** an end-to-end graph test: it does not invoke `code_graph_scan`, `code_graph_query`, or `code_graph_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-081.md:151:2. **Auto-enrichment testing** should extend the `dual-scope-hooks` pattern once graph/CocoIndex auto-enrichment exists, rather than creating a suite around currently-missing `GRAPH_AWARE_TOOLS` behavior.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-002.md:8:2. Non-hook CLIs already receive some guidance via MCP, not only via instruction files, but that MCP guidance is generic recovery/bootstrap guidance rather than active search-tool routing. `CODEX.md` explicitly says Codex does not have hook-based context injection and must manually recover with `memory_context(...resume...)` and `code_graph_status()`, but it also says the MCP server auto-primes on the first tool call. The same pattern appears in the context-prime agent docs: the agent calls `session_resume()` and `session_health()` to emit a compact Prime Package, but the package is framed as session/bootstrap context rather than a tool-routing policy. [SOURCE: CODEX.md:7-12] [SOURCE: CODEX.md:16-27] [SOURCE: CODEX.md:35-54] [SOURCE: .opencode/agents/context-prime.md:24-39] [SOURCE: .opencode/agents/context-prime.md:57-66]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-002.md:12:4. The PrimePackage content is operationally useful but too weak for routing enforcement. It contains `specFolder`, `currentTask`, `codeGraphStatus`, `cocoIndexAvailable`, and `recommendedCalls`. The `recommendedCalls` logic only suggests `code_graph_scan`, `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`, or `memory_match_triggers({ prompt: "<your task>" })`. It never emits the missing decision rule: semantic/concept search -> CocoIndex, structural/call/import analysis -> Code Graph, exact token/path lookup -> Grep/Glob. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:321-363]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-002.md:14:5. `buildServerInstructions()` is the only startup-scoped MCP instruction channel investigated that could reach all runtimes uniformly, but it currently advertises memory inventory and session recovery only. It emits indexed-memory counts, channel availability, memory tool names, and a short session-recovery digest with recommendations like `call session_resume()`, `run code_graph_scan`, or `call memory_context(resume)`. It does not mention CocoIndex/Code Graph routing rules at all, and the file comment states these instructions are computed once at startup and not refreshed during the session. For non-hook CLIs, this is the clearest MCP-wide place where routing guidance could exist but currently does not. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:602-645]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-002.md:16:6. The server has response-hint plumbing, but it currently reinforces surfaced memory/session state, not tool-routing correction. `appendAutoSurfaceHints()` only injects counts/timing for constitutional and triggered memories. `injectSessionPrimeHints()` only adds hints for constitutional-memory count, active spec folder, code graph availability, CocoIndex availability, and recommended next calls. No investigated hook or response-hint code path currently classifies a query as semantic vs structural vs exact-match and redirects accordingly. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/response-hints.ts:86-140] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:530-565] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:813-839]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-002.md:20:8. Runtime instruction coverage is uneven, which explains why non-hook guidance quality differs by CLI. `CODEX.md` contains an explicit query-intent routing table mapping semantic discovery to CocoIndex and structural navigation to Code Graph. By contrast, `GEMINI.md` and root `CLAUDE.md` strongly say "try CocoIndex before Grep/Glob" and define a Copilot/Gemini session-start recovery sequence, but the investigated runtime docs do not carry the same explicit structural-routing matrix inside the MCP-delivered path. The generic `context-prime` agent output format also omits any routing decision tree and instead focuses on spec folder, blockers, graph health, and next steps. [SOURCE: CODEX.md:28-54] [SOURCE: GEMINI.md:69-113] [SOURCE: CLAUDE.md:69-113] [SOURCE: .opencode/agents/context-prime.md:114-133]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-002.md:22:9. The key information currently lost for non-hook CLIs is the actionable routing rule itself at the moment of tool choice. Non-hook runtimes can recover session context through instruction files and MCP bootstrap metadata, but the investigated MCP surfaces do not currently say: use CocoIndex for semantic/code-understanding requests, use Code Graph for structural/caller/import/impact questions, and reserve Grep/Glob for exact text or known-path lookups. As a result, non-hook CLIs receive availability/status signals without the higher-priority behavioral rule that should govern tool selection. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:321-363] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:602-645] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/response-hints.ts:86-140] [SOURCE: CODEX.md:28-33] [SOURCE: GEMINI.md:78-113]
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/plan.md:85:Systematically fix all identified bugs in the system-spec-kit skill and spec_kit commands, prioritizing critical architectural issues and production-breaking defects (missing await in memory_search) before addressing documentation mismatches and minor inconsistencies. Each phase delivers independently verifiable improvements. The full issue inventory is in `research/research.md` and must be treated as the source of truth.
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/plan.md:398:#### 1.5 Fix Missing await in memory_search (REQ-FUNC-031)
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/plan.md:620:- memory_search: includeContent=true returns resolved results
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:9:1. The live PreCompact-style compaction path is currently an in-band MCP pre-dispatch hook, not an implemented external Claude hook script. The runtime chain starts at `context-server.ts` `CallToolRequestSchema`, checks whether the incoming call is `memory_context` with `mode === 'resume'`, extracts a context hint, and routes that hint through `autoSurfaceAtCompaction(contextHint)` before the tool handler runs. `autoSurfaceAtCompaction()` only trims/validates the string and delegates to `autoSurfaceMemories(sessionContext.trim(), 4000, 'compaction')`. `autoSurfaceMemories()` then calls `getConstitutionalMemories()`, `triggerMatcher.matchTriggerPhrases(contextHint, 5)`, enriches constitutional hits with retrieval directives, and finally passes the assembled payload through `enforceAutoSurfaceTokenBudget(...)`. The returned value is either `null` or an `AutoSurfaceResult` object; nothing in this chain writes cache files or produces human-readable hook text by itself. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:325-356`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:188-228`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:300-317`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:978-1009`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:15:4. The current repo does not yet contain the external `PreCompact` and `SessionStart(source=compact)` hook scripts described by the packet; those paths are still spec-level design. Phase 1 defines the intended flow as `compact-precompute.js` reading transcript tail, calling `autoSurfaceAtCompaction(context)`, writing `.claude/compact-context-cache.json`, and emitting no stdout, followed by `compact-inject.js` reading that cache, emitting cached context to stdout, and deleting the cache after injection. Phase 2 refines the same SessionStart-side behavior into a shared `session-prime.ts` that reads pending compact state, outputs cached context for `source=compact`, and falls back to `memory_context({ mode: "resume", profile: "resume" })` for resume-style recovery. There is also an important packet-level mismatch: Phase 1's fallback text omits `profile: "resume"`, but DR-007 and Phase 2 say every resume path must pass it. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:17-31`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:35-49`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:50-66`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:29-53`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:58-74`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:31:   memory_context tool call
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:36:   -> createMCPSuccessResponse(memory_search envelope)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:38:   -> createMCPResponse(memory_context outer envelope)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:43:   In Branch A, constitutional rows come directly from `memory_index` via SQL in `getConstitutionalMemories()`, while trigger matches come from a cached loader query over `memory_index` in `trigger-matcher.ts`. In Branch B, the search pipeline formats result rows into a `memory_search` envelope, then the resume profile rewrites that inner envelope into `{ state, nextSteps, blockers, topResult }`, and only after that does `handleMemoryContext()` wrap the nested search envelope in the outer `memory_context` response. Recovery payloads from `recovery-payload.ts` can appear on the search side when results are empty or weak, but they are not part of `autoSurfaceAtCompaction()` itself. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:90-124`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:195-223`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:176-195`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:337-440`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:621-692`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:688-717`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1215-1280`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:784-835`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1066-1084`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:394-427`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:593-680`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:356-370`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:447-498`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:179-224`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:65:   - Resume fallback path: use `memory_context({ mode: "resume", profile: "resume" })` via the MCP tool contract, because there is no public hook-safe export for `handleMemoryContext()` in `api/`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:67:   In other words, the hook scripts can import the auto-surface primitive directly, but not the whole `memory_context` orchestration contract through the public JS API. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:67-84`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:300-317`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/api/README.md:24-25`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:10-17`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:45-48`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:69-74`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:113:CallToolRequest(memory_context, mode='resume')
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:137:-> fallback to memory_context(..., profile:'resume') when cache missing
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:163:- the exact live runtime seam is the `memory_context(mode:'resume')` pre-dispatch branch in `context-server.ts`, not an already-existing external Claude hook script;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:177:3. Normalize the packet’s SessionStart fallback contract to `memory_context({ mode: "resume", profile: "resume" })` everywhere. The decision record and Phase 2 already require that; Phase 1 should be brought into line before implementation starts. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:58-66`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:45-48`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:69-74`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:181:   - SessionStart(compact) should prefer cache, then fall back to profiled `memory_context`, and only then emit a minimal constitutional-safe message if both fail.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-034.md:184:5. Document the two-layer output model in the implementation notes: compaction auto-surface lives in outer envelope metadata, while the resume brief lives inside the nested `memory_search` envelope. That distinction matters for both hook rendering and debugging. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:393-399`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1247-1280`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:356-370`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:447-498`]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-003.md:2:## Focus: Analyze query classification patterns that distinguish semantic discovery (CocoIndex), structural navigation (Code Graph), and exact-text/path lookup (Grep/Glob), then design a lightweight routing classifier.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-003.md:5:1. The MCP server already contains a lightweight structural-vs-semantic classifier, but it is only a 3-state `structural | semantic | hybrid` heuristic and is currently used inside `memory_context`, not as a universal first-tool router. `classifyQueryIntent()` scores keyword hits at 1x, regex-pattern hits at 2x, and picks a dominant class only when one side exceeds 65% of the total score; otherwise it falls back to `hybrid`. `memory_context` then uses that result to optionally attach code-graph context for `structural` or `hybrid` queries, while `semantic` or low-confidence queries simply fall through to the existing semantic path. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:11-19] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:21-77] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:118-179] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1087-1161]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-003.md:9:3. Semantic queries are characterized by concept, behavior, or intent language: the user wants examples, patterns, implementations, purpose, or explanation rather than graph edges. The existing classifier already keys on terms like `similar`, `related`, `example`, `pattern`, `usage`, `approach`, `strategy`, `find`, `search`, `discover`, `explain`, `understand`, `purpose`, `concept`, and domain concepts such as `authentication`, `middleware`, or `validation`, along with patterns like `find code ... about`, `implementations of`, `examples of`, and `what is the pattern/purpose`. Runtime guidance matches this: `CODEX.md` routes semantic discovery such as `find code that...` and `how is X implemented` to CocoIndex, `GEMINI.md` says concept/intent queries and unfamiliar code exploration should use CocoIndex first, and `ccc_status` explicitly says `Use mcp__cocoindex_code__search for semantic queries.` [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:44-58] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:69-77] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:36-46] [SOURCE: CODEX.md:28-33] [SOURCE: GEMINI.md:78-104] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/handlers/code-graph/ccc-status.ts:35-39]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-003.md:20:6. For Q9, server-instruction changes remain the highest-leverage enforcement surface, tool-description changes are second, and response hints are corrective-only. `buildServerInstructions()` is pushed through `setInstructions(...)` before transport is connected, so it is the only investigated server-wide, pre-tool-choice injection point. `ListToolsRequestSchema` returns `TOOL_DEFINITIONS`, so tool descriptions are also visible before selection, but only for this MCP server's tools; they cannot fully steer CocoIndex because it is a separate provider. By contrast, PrimePackage hints are injected only after a tool call succeeds, so they can improve the second choice but cannot prevent the first misroute. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:605-646] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:555-557] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:685-687] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:833-839]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-003.md:22:7. The practical enforcement shape is now clear: put the 3-way/4-way routing rule into `buildServerInstructions()` as the universal policy, mirror concise structural-vs-semantic trigger wording in `tool-schemas.ts` and the CocoIndex-side description where available, and use response hints only as recovery guidance after a misroute. The classifier does not need to hard-dispatch tools; it only needs to produce routing hints like `exact_text -> grep/glob`, `semantic -> CocoIndex`, `structural -> code_graph_query/context`, `hybrid -> CocoIndex first, then graph enrichment if graph healthy`. That keeps false redirects low while giving all runtimes the same pre-selection decision rubric. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:605-646] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:637-739] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:530-565] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:833-839]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:1:# Iteration 017: memory_context Resume Flow Analysis
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:5:This iteration traced the live `memory_context` resume path from MCP request handling down to the profiled search payload returned to the caller. The requested file `.opencode/skills/system-spec-kit/mcp_server/lib/context-server.ts` does not exist in the current tree, so the analysis used the actual entrypoint `.opencode/skills/system-spec-kit/mcp_server/context-server.ts` together with all `.ts` files under `mcp_server/api/`, `hooks/memory-surface.ts`, and the directly connected implementation files that own the resume behavior.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:9:1. `memory_context({ mode: 'resume', profile: 'resume' })` does not return a flat resume brief as the top-level tool payload. The final tool return is an outer MCP transport wrapper, whose `content[0].text` is a JSON `MCPEnvelope`, and that outer envelope's `data` is a `ContextResult` object containing orchestration metadata plus a nested `content[0].text` string from `memory_search`. In resume mode, the inner `memory_search` envelope is where the profiled resume brief appears. The outer `memory_context` envelope still keeps `strategy`, `mode`, `resumeAnchors`, and optional `systemPromptContext*` fields on `data`, not `state/nextSteps/blockers` directly. `[.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:688-717] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1247-1279] [.opencode/skills/system-spec-kit/mcp_server/lib/response/envelope.ts:16-35] [.opencode/skills/system-spec-kit/mcp_server/lib/response/envelope.ts:264-282] [.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:86-112] [.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:447-497]`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:11:2. `profile: 'resume'` changes the output format only inside the nested `memory_search` envelope. `handleMemoryContext()` forwards `profile` to `handleMemorySearch()`, and `handleMemorySearch()` applies `applyProfileToEnvelope()` as a best-effort post-processing step. That formatter removes `data.results`, preserves other non-result data fields, adds `data.state`, `data.nextSteps`, `data.blockers`, and `data.topResult`, and stamps `meta.responseProfile = 'resume'`. Without `profile`, the inner envelope keeps the standard search shape with `data.results`. The outer `memory_context` envelope is not flattened into the resume brief. `[.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:246-259] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1066-1084] [.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:283-286] [.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:356-370] [.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:447-497]`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:41:   -> createMCPResponse() for outer memory_context envelope
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:46:   The `api/*.ts` files are not in this runtime call chain; they are public re-export barrels for external scripts and indexing/search bootstrapping, not live request middleware for `memory_context`. `[.opencode/skills/system-spec-kit/mcp_server/context-server.ts:308-440] [.opencode/skills/system-spec-kit/mcp_server/tools/index.ts:24-35] [.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:10-17] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:872-892] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:980-1354] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1066-1084] [.opencode/skills/system-spec-kit/mcp_server/api/index.ts:11-117] [.opencode/skills/system-spec-kit/mcp_server/api/indexing.ts:26-57]`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:48:5. `autoSurfaceAtCompaction()` integrates with resume mode in the server layer, not inside `handleMemoryContext()`. `context-server.ts` explicitly treats `memory_context` calls with `args.mode === 'resume'` as `isCompactionLifecycleCall`, then routes them through `autoSurfaceAtCompaction(contextHint)` before dispatch. That hook uses the compaction token budget and returns surfaced constitutional/triggered memories. After the tool handler returns, the server appends an auto-surface hint into the outer envelope and also stores the full surfaced payload in `meta.autoSurfacedContext`. This is separate from the handler-level auto-resume working-memory injection. `[.opencode/skills/system-spec-kit/mcp_server/context-server.ts:325-347] [.opencode/skills/system-spec-kit/mcp_server/context-server.ts:373-399] [.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:283-317] [.opencode/skills/system-spec-kit/mcp_server/hooks/response-hints.ts:59-104] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1219-1239]`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:53:   - L1 tool-layer budget: `2000` tokens for `memory_context` from `layer-definitions.ts`. `context-server.ts` writes this value into the outer envelope's `meta.tokenBudget` after the handler returns.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:82:Source: the outer transport wrapper always serializes a single JSON envelope into `content[0].text`, and `memory_context` uses `createMCPResponse()` for its final payload. `[.opencode/skills/system-spec-kit/mcp_server/lib/response/envelope.ts:30-35] [.opencode/skills/system-spec-kit/mcp_server/lib/response/envelope.ts:264-282] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1247-1279]`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:84:### 2. Effective outer `memory_context` data shape in resume mode
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:91:  content: Array<{ type: 'text'; text: string }>; // nested memory_search envelope
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:103:This is the object placed in the outer envelope's `data`. The nested `content[0].text` is the profiled `memory_search` envelope. `[.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:688-717] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1228-1239]`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:116:Applied by `memory_search` when `profile: 'resume'` is forwarded from `memory_context`. `[.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:86-92] [.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1066-1084]`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:125:      "text": "{\n  \"summary\": \"Context retrieved via resume mode (resume strategy)\",\n  \"data\": {\n    \"strategy\": \"resume\",\n    \"mode\": \"resume\",\n    \"resumeAnchors\": [\"state\", \"next-steps\", \"summary\", \"blockers\"],\n    \"content\": [\n      {\n        \"type\": \"text\",\n        \"text\": \"{\\n  \\\"summary\\\": \\\"...search summary...\\\",\\n  \\\"data\\\": {\\n    \\\"count\\\": 5,\\n    \\\"state\\\": \\\"...\\\",\\n    \\\"nextSteps\\\": [...],\\n    \\\"blockers\\\": [...],\\n    \\\"topResult\\\": {...}\\n  },\\n  \\\"meta\\\": {\\n    \\\"tool\\\": \\\"memory_search\\\",\\n    \\\"responseProfile\\\": \\\"resume\\\"\\n  }\\n}\"\n      }\n    ],\n    \"systemPromptContextInjected\": true,\n    \"systemPromptContext\": [...]\n  },\n  \"meta\": {\n    \"tool\": \"memory_context\",\n    \"mode\": \"resume\",\n    \"tokenBudget\": 2000,\n    \"tokenBudgetEnforcement\": {\n      \"budgetTokens\": 1200\n    },\n    \"sessionLifecycle\": {\n      \"resumed\": true\n    }\n  }\n}"
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:141:- the resume brief lives in the inner `memory_search` envelope, not the outer `memory_context` envelope;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:143:- `memory_context(mode:'resume')` is specially routed through the compaction auto-surface hook before dispatch;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:152:1. Treat the resume brief as an inner-envelope contract unless you intentionally add a flattening layer. If Hybrid Context Injection expects direct `{ state, nextSteps, blockers }` access from `memory_context`, it will currently parse the wrong level.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:156:   - `memory_context layer budget = 2000`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:164:5. Consider renaming or documenting the `isCompactionLifecycleCall` branch more explicitly. Today it is triggered by `memory_context(mode:'resume')`, which is accurate in code but easy to misread as a literal session-compaction event.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-017.md:166:6. If downstream consumers need the auto-resume working-memory hints, read them from the outer `memory_context` envelope (`systemPromptContext*`), not from the inner profiled search payload. The two injections happen at different layers and should remain distinct in any hook graph.
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/spec.md:92:| CocoIndex Integration | Context Enrichment | CocoIndex provides semantic code search complementing structural code graph and memory context |
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/spec.md:116:- Reference CocoIndex Code MCP as companion system for semantic code search
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/spec.md:117:- Document the complementary architecture: CocoIndex (semantic) + Code Graph (structural) + Memory (session)
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/spec.md:126:- Three-system integration diagram showing CocoIndex, Code Graph, and Memory as parallel context sources
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/spec.md:179:Phases 008-025 implemented the Code Graph system (4 MCP tools, 3 CCC tools, 3 session tools, tree-sitter indexer, CocoIndex bridge, budget allocator, auto-trigger, query routing) but documentation was never updated to reflect these additions. Analysis using Copilot CLI GPT-5.4 review agents + direct file inspection confirmed **10 MCP tools completely undocumented** in user-facing docs.
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/plan.md:138:   - Complementary design: CocoIndex (semantic) + Code Graph (structural) + Memory (session)
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/plan.md:141:   - Query routing: structural → code_graph, semantic → CocoIndex, session → Memory
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/plan.md:180:   - CocoIndex seed resolution flow
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:2:## Focus: Draft implementation-ready PrimePackage routing directives and session snapshot routing state so hook-compatible and non-hook CLIs share the same CocoIndex-vs-Code-Graph routing policy after bootstrap and during recovery.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:21:    'Use CocoIndex first for semantic, intent-based, or unfamiliar-code discovery.',
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:32:      'Code graph is not ready: prefer CocoIndex for discovery until code_graph_scan restores graph freshness.',
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:38:      'CocoIndex is unavailable: rely on code_graph_* for structure and rg/glob for exact lookup.',
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:45:      'Use CocoIndex for semantic discovery, then use code_graph_query/code_graph_context for structural follow-up.';
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:48:      'Use CocoIndex first; run code_graph_scan before depending on code_graph_query/code_graph_context.';
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:51:      'CocoIndex unavailable: use code_graph_query/code_graph_context for structural exploration and rg/glob for exact lookup.';
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:54:      'CocoIndex unavailable and code graph not ready: use rg/glob for exact lookup, then run code_graph_scan before structural analysis.';
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:107:  const cocoIndexAvailable = isCocoIndexAvailable();
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:115:    recommendedCalls.push('memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })');
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:118:    recommendedCalls.push('memory_match_triggers({ prompt: "<your task>" })');
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:164:    cocoIndexAvailable = isCocoIndexAvailable();
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:252:    hints.push(`Code graph: ${pkg.codeGraphStatus}, CocoIndex: ${pkg.cocoIndexAvailable ? 'available' : 'not installed'}`);
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:276:  lines.push(`- CocoIndex: ${snap.cocoIndexAvailable ? 'available' : 'unavailable'}`);
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:283:1. `PrimePackage` is still the correct post-selection intervention point for second and later tool decisions, but its current payload is missing actual routing policy. Today it only carries `specFolder`, `currentTask`, `codeGraphStatus`, `cocoIndexAvailable`, and `recommendedCalls`, and `recommendedCalls` only suggests bootstrap or maintenance actions such as `code_graph_scan`, `memory_context(...resume...)`, or `memory_match_triggers(...)`. That means the package exposes environment state but not the semantic-vs-structural-vs-exact-match rule the model needs after the first tool call. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:64-70] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:316-364]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:284:2. The cleanest implementation is to synthesize `routingRules` from the same two signals already available in `buildPrimePackage()`: code graph freshness and CocoIndex availability. This keeps PrimePackage lightweight, deterministic, and directly aligned with the root-cause routing decision: semantic discovery -> CocoIndex, structural traversal -> Code Graph, exact lookup -> `rg`/`glob`, with a stale-graph fallback back to CocoIndex. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:335-363]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:288:6. The session snapshot change only matters if startup/server instructions consume it. `buildServerInstructions()` currently computes a local `recommended` string from primed/graph/session-quality heuristics, but it does not carry any explicit CocoIndex-vs-Code-Graph routing statement. Replacing that local synthesis with `snap.routingRecommendation` is the smallest change that makes the same routing policy visible during non-hook CLI recovery before the next tool choice. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts:627-645] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:53-105]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-007.md:292:- Answered the PrimePackage extension question: add `routingRules: string[]` and populate it from code graph freshness + CocoIndex availability.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-106.md:5:`@context-prime` is a read-only bootstrap subagent designed to recover memory context, assess code-graph/CocoIndex health, score session health, and return a Prime Package. It is explicitly optimized for fast, best-effort execution: under 30 seconds, and if a tool fails it skips that step and reports it as unavailable. [SOURCE: `.opencode/agents/context-prime.md`]
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/checklist.md:191:- [x] CHK093 [P0] memory_search awaits formatSearchResults (no Promise objects returned) | Evidence: Added `await` at lines 1085, 1140, 1161 in context-server.js
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/checklist.md:303:- [x] CHK084 [P0] `memory_search` tool returns results | Evidence: Search functionality verified
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/checklist.md:307:- [x] CHK088 [P1] `memory_match_triggers` identifies relevant memories | Evidence: Trigger matching verified
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:17:`opencode.json` registers 4 MCP servers directly: `sequential_thinking`, `spec_kit_memory`, `cocoindex_code`, and `code_mode`. All use `"type": "local"` with command arrays. The `spec_kit_memory` server provides all memory tools (memory_context, memory_search, code_graph_scan, code_graph_query, etc.). The `cocoindex_code` server provides semantic code search.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:19:Critical finding: Both code_graph and CocoIndex tools are already available to ALL agents via MCP -- the barrier is not availability but INVOCATION. No agent currently auto-calls `code_graph_scan` or `ccc_reindex` at session start because there is no lifecycle hook to trigger them.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:24:Commands in `.opencode/commands/spec_kit/` are YAML-based workflow definitions (e.g., `resume.md`, `complete.md`, `plan.md`, `implement.md`). The `/spec_kit:resume` command (spec_kit_resume_auto.yaml) already implements session detection, memory loading, and progress calculation -- but focuses purely on memory context, not code graph or CocoIndex.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:31:The @context agent is the "exclusive entry point for ALL exploration tasks" -- every codebase search routes through it. Its 3-layer retrieval (Memory -> Codebase -> Deep Memory) currently does NOT include code graph or CocoIndex as automatic layers. Adding code_graph_context as a Layer 1.5 (between Memory and Codebase) would mean every exploration automatically benefits from structural graph data.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:45:Current:  memory_match_triggers -> memory_context -> memory_search -> CocoIndex -> Glob -> Grep -> Read
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:46:Proposed: memory_match_triggers -> memory_context -> code_graph_context(seeds from memory) -> CocoIndex search -> memory_search -> Glob -> Grep -> Read
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:50:- After `memory_context(deep)`, call `code_graph_context({ queryMode: "neighborhood", input: <topic> })` to get structural context
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:51:- Feed code_graph results as seeds into CocoIndex for enriched semantic search
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:61:  purpose: Ensure code graph and CocoIndex indices are fresh
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:65:    - Check ccc_status() for CocoIndex readiness
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:66:    - If CocoIndex stale, trigger ccc_reindex({ full: false })
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:91:Implementation: In `context-server.ts`, add a `sessionPrimed` flag. On first `memory_context` or `memory_match_triggers` call, check `code_graph_status` internally and trigger incremental scan if stale. This is invisible to the caller and works identically across all runtimes.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:103:| CocoIndex auto-reindex | Hook triggers on file changes | Resume command + CLAUDE.md instruction | Tier B + C |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-065.md:135:Consolidation iteration: Synthesize all Q13-Q16 findings into a prioritized feature improvement roadmap. The 4-tier OpenCode integration design (this iteration) should be merged with the 3-tier auto-enrichment design (iteration 057), the non-hook runtime UX tiers (iteration 058), and the CocoIndex improvements (iteration 059) into a single implementation priority matrix.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:3:## Focus: Draft updated runtime instruction file sections that replace passive CocoIndex/Code Graph guidance with short active decision trees that are harder for AI assistants to skip across hook-compatible and non-hook CLIs.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:9:IF the task asks by concept, intent, behavior, or unfamiliar code, THEN start with CocoIndex.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:11:IF code graph status is stale, empty, or unavailable, THEN skip graph tools and use CocoIndex plus direct file reads until graph health recovers.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:17:IF the request is semantic discovery, implementation lookup, or unfamiliar-code exploration, THEN start with CocoIndex.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:19:IF `code_graph_status()` shows stale, empty, or unavailable graph state, THEN do not use graph tools yet; use CocoIndex plus direct reads first.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:25:IF the task is concept search, intent search, behavior lookup, or unfamiliar code, THEN start with CocoIndex.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:27:IF the graph is stale, empty, or unavailable, THEN fall back to CocoIndex plus direct file reads until graph-backed retrieval is trustworthy again.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:31:IF hook-injected context is present, THEN keep it and still route code search by query type.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:34:IF the task is semantic discovery or unfamiliar code, THEN start with CocoIndex.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:36:IF graph status is stale, empty, or unavailable, THEN use CocoIndex plus direct reads instead of graph tools.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:39:1. Root `CLAUDE.md` already contains CocoIndex-first guidance, but the current phrasing is still passive enough to compete with a model's built-in Grep/Glob bias. The file says CocoIndex "**MUST use**" for unfamiliar code and concept/intent search, while the nearby quick-reference table still reads more like descriptive workflow guidance than a hard decision tree. [SOURCE: CLAUDE.md:34-37] [SOURCE: CLAUDE.md:46-50]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:40:2. Root `CODEX.md` already has the strongest runtime-specific routing structure because it separates semantic discovery from structural navigation. Its `Query-Intent Routing` section maps semantic discovery to CocoIndex and structural navigation to `code_graph_query` / `code_graph_context`, and its session-start section already ties structural retrieval to graph health. [SOURCE: CODEX.md:14-20] [SOURCE: CODEX.md:28-33]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:41:3. Root `GEMINI.md` already includes the clearest search-routing tree in the repository: exact text goes to Grep, known paths go to Glob, concept/intent goes to CocoIndex, and unfamiliar code also starts with CocoIndex. It also already states the needed graph fallback rule: if graph state is stale, empty, or unavailable, the runtime should use CocoIndex plus direct file reads until graph-backed retrieval is trustworthy. [SOURCE: GEMINI.md:69-75] [SOURCE: GEMINI.md:78-113]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:44:6. The most consistent cross-runtime fix is not to invent new guidance per file, but to normalize all runtime docs around the same five-step decision order: exact literal -> Grep, known path -> Glob, semantic discovery -> CocoIndex, structural graph question -> Code Graph, stale graph -> CocoIndex plus direct reads. That keeps the escape hatch for exact text while making Grep/Glob secondary instead of default. [SOURCE: CLAUDE.md:46-50] [SOURCE: CODEX.md:28-33] [SOURCE: GEMINI.md:78-113]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:45:7. The replacement sections should use active `IF/THEN` language because the current passive phrasing ("MUST use", "try CocoIndex first") still leaves room for models to interpret Grep/Glob as the safer default. The Gemini tree and Codex query-intent split provide the strongest source patterns for converting these rules into explicit branching logic. [SOURCE: CLAUDE.md:34-37] [SOURCE: CODEX.md:28-33] [SOURCE: GEMINI.md:80-113]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-008.md:48:- Q8: What replacement runtime instruction text should be drafted to enforce CocoIndex/Code Graph routing more actively across CLAUDE.md, CODEX.md, GEMINI.md, and `.claude/CLAUDE.md`?
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-096.md:16:The recovery/session plumbing already exists. `memory_context` mints or validates a trusted session id, persists session state, computes resume heuristics, and can inject prior working-memory prompt context when `mode=resume` on a resumed session. `session-manager.ts` can also save and recover persisted `spec_folder`, `current_task`, `context_summary`, and `pending_work`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:783-816`; `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1117-1217`; `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1291-1312`; `.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1020-1076`; `.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1126-1180`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-096.md:18:The doc/gate side is already partly in place. Root `CLAUDE.md` and `AGENTS.md` tell Copilot/Gemini sessions to call `memory_context(...resume...)` and `code_graph_status()` on the first turn; `CODEX.md` does the same for Codex; `.claude/CLAUDE.md` says Claude should trust hook payloads first; Gemini is configured to load `GEMINI.md` and `AGENTS.md`, while `.codex/config.toml` only configures MCP servers and does not itself provide a first-turn instruction slot. [SOURCE: `CLAUDE.md:69-76`; `AGENTS.md:69-76`; `CODEX.md:14-20`; `.claude/CLAUDE.md:5-23`; `.gemini/settings.json:8-13`; `.codex/config.toml:5-39`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-096.md:28:- Description: Upgrade the existing `primeSessionIfNeeded()` path from "metadata-only first-call hinting" into a real priming payload builder. On the first tool call in a fresh MCP process/session, inject a compact `session_context` block containing recovered session state (`specFolder`, `currentTask`, `pendingWork` if available), code-graph health, and explicit next actions (`memory_context resume`, `code_graph_status`). Do this centrally in `context-server.ts`, not per tool.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-096.md:35:- Dependencies: Reuse existing `primeSessionIfNeeded()`, `getCodeGraphStatusSnapshot()`, and `session-manager` recovery/state APIs; avoid recursive calls back into `memory_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-096.md:41:- Description: Normalize and harden first-turn instructions in `AGENTS.md`, `CLAUDE.md`, `CODEX.md`, and `GEMINI.md` so they all use the same mandatory sequence: `memory_context(...resume...)` then `code_graph_status()`, then fallback to CocoIndex/file reads if graph is stale. Optionally mirror this same wording in MCP `buildServerInstructions()`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-096.md:96:2. Populate that payload from existing `session-manager` recovery fields plus code-graph snapshot; do not recurse through `memory_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:1:# Iteration 046: CocoIndex ↔ Code Graph Bridge Design
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:5:Define the bridge contract between CocoIndex semantic retrieval and the planned structural code graph so the two systems can enrich each other bidirectionally without collapsing into one store. This iteration answers the open design questions left by DR-010: seed shape, expansion behavior, reverse enrichment, end-to-end flow, merge strategy, failure handling, and latency budget for `PreCompact`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:11:   The bridge should accept CocoIndex hits in their native shape because DR-010 explicitly says CocoIndex remains the semantic system of record while code graph remains structural. CocoIndex already returns `file path + line range + snippet + relevance + language`; forcing an intermediate symbol-resolution tool would add latency, duplicate work, and make the bridge awkward at the exact point where the two systems meet. Our own MCP conventions also already distinguish deterministic low-level tools from higher-level orchestration tools, so `code_graph_context` is the right place to accept richer seed shapes and normalize them internally. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:94-105`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/spec.md:40-46`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:154-264`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:39-43`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:68:   Given a CocoIndex hit at `file X lines 10-30`, the most useful expansion is not "walk everything within two hops." The useful order is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:90:3. Reverse enrichment should use graph neighborhoods to generate scoped semantic queries, not simply re-run CocoIndex on the original prompt.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:108:   CocoIndex returns 2-5 semantically similar but structurally distinct snippets.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:121:   `mcp__cocoindex_code__search("how does authentication work", limit=5)` and a graph bootstrap over explicit anchors or current working-set files.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:123:   3. Normalize CocoIndex hits into `CodeGraphSeed[]`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:134:   7. If the neighborhood is thin or overly local, synthesize a scoped semantic augmentation query from the neighborhood and ask CocoIndex for 2-5 analogs outside the already-covered ranges.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:145:   A purely sequential design (`CocoIndex -> graph -> done`) is too dependent on semantic hits being immediately correct and wastes cheap structural cues we may already have from the current file or active working set. A purely parallel design (`query both and merge blindly`) misses the actual bridge value because the second system never gets to use the first system's output as a focused seed.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:151:   Stage B, sequential: use CocoIndex hits to drive structural expansion and use graph neighborhoods to drive semantic augmentation.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:171:   Failure mode: CocoIndex returns irrelevant hits.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:175:   Mitigation: return the CocoIndex snippet plus file outline fallback, mark `freshness.partial = true`, and optionally refresh the graph only for the affected file or package. This matches the packet's hybrid freshness model rather than forcing a repo-wide rebuild. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:266-270`] [SOURCE: https://docs.continue.dev/guides/custom-code-rag]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:178:   Mitigation: preserve a single-system response with a warning section. If CocoIndex is down, graph-only context should still work for explicit files/symbols. If graph is down, semantic hits should still return raw snippets and file anchors without pretending to have structural validation.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:200:   450-700 ms: CocoIndex semantic search, hard-capped at 800 ms.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:231:   CocoIndex hits become `ArtifactRef` plus semantic metadata.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:271:Iterations 036-045 established the separation between semantic and structural retrieval, the code-graph API shape, and the compaction-oriented late-fusion architecture. What they did not settle was the bridge itself: exactly what `code_graph_context` should accept from CocoIndex, how graph expansion should be budgeted around a semantic seed, how structural neighborhoods should generate semantic enrichment in the reverse direction, and how to make all of that fit a 2-second `PreCompact` window. This iteration adds those missing contracts and execution rules. The most novel points are the direct `seeds[]` contract, the staged parallel-then-sequential execution model, the reverse semantic augmentation design, the explicit failure degradations, and the concrete latency split.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-046.md:275:1. Add `seeds?: CodeGraphSeed[]` to `code_graph_context` and treat file-range seeds as the primary CocoIndex bridge surface.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:3:## Focus: Design the `context-prime` routing output so it reinforces CocoIndex vs Code Graph vs exact-search selection across runtimes, and define the unit, integration, and manual tests needed to verify end-to-end enforcement.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:29:- **Semantic / intent discovery** -> CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:32:- **Bridge** -> CocoIndex results can seed `code_graph_context`
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:33:- **Fallback** -> If code graph is stale/empty, prefer CocoIndex until `session_resume()` or `code_graph_scan`
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:41:Need code search?
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:43:  concept/meaning/"how does X work" -> CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:45:  code graph stale or empty -> CocoIndex first, then session_resume / code_graph_scan
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:46:  semantic result needs structure -> feed CocoIndex result into code_graph_context
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:55:   - semantic language points to CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:65:   - fresh graph + CocoIndex available -> normal semantic/structural/exact routing rules
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:66:   - stale graph -> fallback text points to CocoIndex plus `code_graph_scan`
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:68:   - CocoIndex unavailable -> semantic route marked unavailable or downgraded explicitly
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:76:   - a compact routing hint in `hints`, e.g. `Routing: semantic -> CocoIndex; structural -> Code Graph; exact -> rg/glob`
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:84:   - Expected first tool: CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:90:   - Expected behavior: use CocoIndex first or recommend `session_resume()` / `code_graph_scan` instead of forcing Code Graph
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:95:- **Codex CLI**: verify non-hook fallback still receives startup/server-instruction routing text and then chooses CocoIndex, Code Graph, or rg/glob appropriately. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/code-graph/runtime-detection.ts:30-33]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:103:2. PrimePackage is the right place to store structured routing metadata, but not the right place to hide all routing logic inside `recommendedCalls`. Today `recommendedCalls` mixes operational recovery suggestions (`code_graph_scan`, `memory_context(...)`) with lightweight next steps, so it should remain imperative while a new `routingRules` field carries the actual policy. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:351-363]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:104:3. The routing taxonomy should reuse the architecture’s existing split: semantic discovery -> CocoIndex, structural navigation -> Code Graph, session continuity -> Memory. For enforcement purposes, the PrimePackage should add a fourth visible category for exact text/path lookup -> rg/glob, because that is the missing contrast against CocoIndex overuse and Graph overuse. [SOURCE: .opencode/skills/system-spec-kit/ARCHITECTURE.md:545-553]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:107:6. PrimePackage population currently has no focused test coverage at all. That is a root testing gap: if `routingRules` is added, the builder needs its own direct unit tests across fresh/stale/empty graph states and CocoIndex availability combinations. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:316-364] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tests]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:110:9. The bridge behavior should be explicitly documented in PrimePackage: semantic discovery often starts in CocoIndex, then pivots into `code_graph_context` for neighborhood, outline, or impact expansion. That bridge is already part of the tool schema and manual testing playbook, so elevating it into routing output closes the gap between discovery and structural follow-up. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:660-693] [SOURCE: .opencode/skills/system-spec-kit/manual_testing_playbook/22--context-preservation-and-code-graph/255-cocoindex-code-graph-routing.md:16-33]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/iterations/iteration-009.md:117:## Next Focus Recommendation: Final iteration should investigate over-aggressive enforcement failure modes and escape hatches: how to avoid false redirects, how to degrade gracefully when CocoIndex or Code Graph is unavailable, and how to specify acceptance criteria for a full implementation patch across startup instructions, PrimePackage, and hint injection.
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/scratch/legacy-memory-quarantine/15-01-26_11-52__bug-analysis-and-fix.md:275:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/064-bug-analysis-and-fix" })` |
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/scratch/legacy-memory-quarantine/15-01-26_11-52__bug-analysis-and-fix.md:280:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:3:description: "AI assistants across all CLI runtimes (Claude Code, Codex CLI, Copilot CLI, Gemini CLI) consistently default to Grep/Glob for code search tasks even when CocoIndex (semantic) an..."
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:26:AI assistants across all CLI runtimes (Claude Code, Codex CLI, Copilot CLI, Gemini CLI) consistently default to Grep/Glob for code search tasks even when CocoIndex (semantic) and Code Graph (structural) are available. The root cause is a **passive instruction model**: CLAUDE.md says "MUST use CocoIndex" but this competes with built-in AI preferences for fast, familiar tools. There is no active enforcement at the MCP layer where tool selection decisions are made.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:70:- Semantic/concept search (how does X work, find code about Y) → CocoIndex (mcp__cocoindex_code__search)
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:73:- CocoIndex: [available/unavailable] | Code Graph: [fresh/stale/empty]
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:74:- If graph stale/empty: prefer CocoIndex until code_graph_scan restores health
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:80:- Populated based on CocoIndex availability + Code Graph freshness
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:87:- `memory_search` called with semantic code query patterns → hint: "Consider CocoIndex for code search"
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:88:- `memory_context` called with structural query patterns → hint: "Consider code_graph_query"
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:94:- Surfaces at top of EVERY `memory_search` result
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:95:- Decision tree: semantic → CocoIndex, structural → Code Graph, exact → Grep
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/research.md:113:| **Semantic** | "find code about", "how does X work", "implementations of", "related to" | CocoIndex |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:1:# Iteration 051: Incremental Index Coordination — CocoIndex + Code Graph Sync
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:5:Determine how our planned structural code graph index should coordinate with the already-deployed CocoIndex semantic index so both stay useful without creating a brittle shared-refresh system. This pass focuses on change detection, watcher strategy, freshness exposure, branch-switch behavior, rebuild cost, and the smallest safe MVP coordination model.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:9:1. CocoIndex should be treated as an independently managed semantic index whose freshness is refreshed through its own daemon and command surfaces, not as a watcher we control directly.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:11:   The local CocoIndex docs are explicit about what is public: `ccc index` performs incremental updates on subsequent runs, `ccc search --refresh` forces a refresh before search, and the MCP `search` tool defaults `refresh_index` to `true`. The same docs also describe a daemon that auto-starts, continues background indexing after client disconnect, and serves search over IPC. What the docs do not document is a public "shared file watcher" contract, a Git-status-based detector, or a stable event stream we should subscribe to. That means the safest implementation assumption is: CocoIndex internally decides how to notice or reconcile file changes, while our integration should rely only on the supported refresh surfaces (`ccc index`, CLI `--refresh`, MCP `refresh_index`) and its reported status/freshness metadata. [SOURCE: `.opencode/skills/mcp-coco-index/references/tool_reference.md:80-104`] [SOURCE: `.opencode/skills/mcp-coco-index/references/tool_reference.md:203-247`] [SOURCE: `.opencode/skills/mcp-coco-index/SKILL.md:265-306`] [SOURCE: `.opencode/skills/mcp-coco-index/SKILL.md:372-377`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:13:   Inference: because the daemon exists and indexing can continue after client disconnect, CocoIndex likely has its own internal scheduling and refresh logic. But the packet evidence does not prove a repo-local file watcher API, so our design should not depend on one.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:21:   Our packet already states that graph-specific incremental updates remain independent of CocoIndex, and the CocoIndex docs describe a daemonized background system with its own concurrency caveats around repeated `refresh_index=true` requests. A shared watcher would create coupling at the least stable seam: event delivery, debounce timing, error propagation, and branch-switch recovery. It also risks turning one indexer's outage into a shared outage. The cleaner design is: each index owns its own refresh cadence, but both publish comparable freshness records that a higher-level orchestration layer can inspect. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:472-487`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:94-105`] [SOURCE: `.opencode/skills/mcp-coco-index/SKILL.md:372-377`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:27:   The packet's API research already recommends that stale graph data should still be returned when useful, but with explicit freshness metadata and warnings, while repair happens in the background or on scoped demand. That same pattern should apply to the combined system. If CocoIndex is fresher than the graph, semantic recall can still seed candidate files while structural expansion is marked stale or partial. If the graph is fresher than CocoIndex, structural neighborhood answers can still be served, but semantic similarity should be marked stale and potentially trigger a CocoIndex refresh on the next semantic query. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:75-125`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:266-277`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:309-332`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:201-205`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:33:   - `semanticFreshness`: CocoIndex state
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:41:   Our packet already frames CocoIndex and the code graph as complementary but independent systems: "what resembles what" versus "what connects to what." That separation argues against a tightly coupled event bus or a single transaction boundary. The graph research also converged on background-first indexing plus scoped repair when stale, which maps naturally to a coordination layer that compares timestamps, pending jobs, and stale flags before deciding whether to use cached results, request a scoped repair, or warn. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:94-105`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:246-263`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:266-277`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:209-209`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:45:   - CocoIndex owns semantic indexing
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:52:   CocoIndex's own skill guidance says to suggest reindexing after branch switches, major refactors, or large merges. The code graph packet independently classifies branch switches, pulls/merges, dependency changes, and grammar/schema changes as broader async rebuild triggers rather than per-save hot-path events. That suggests the coordination rule: on branch switch, both systems mark their freshness as suspect, run reconciliation, and only escalate to full rebuild when the delta is large enough or the index format changed. For the code graph that means scanning changed/deleted/renamed files and using content hashes and invalidation classes; for CocoIndex it means invoking its normal incremental rebuild path rather than assuming a watcher remained valid across checkout. [SOURCE: `.opencode/skills/mcp-coco-index/SKILL.md:345-347`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-041.md:15-19`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:250-255`] [SOURCE: https://git-scm.com/docs/git-status/2.40.0.html]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:54:8. Rebuild cost is asymmetric: CocoIndex is the more expensive index to refresh, while the code graph should be cheaper for scoped updates but still non-trivial for full-project invalidation.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:56:   The CocoIndex docs say first indexing typically takes 1-5 minutes and later runs are incremental. Its pipeline includes scanning, chunk splitting, embedding generation, and vector storage, which is inherently heavier than syntax parsing alone and may also involve remote embedding APIs. By contrast, the code graph's hot path is expected to be "parse one file, extract local symbols/edges, update SQLite," and iteration 041 argues the parser itself is unlikely to be the dominant cost; downstream invalidation and dependency propagation matter more. Iteration 038 adds the strongest concrete Tree-sitter benchmark in the packet: parsing a 2,157-line Rust file in 6.48 ms, with incremental updates generally under 1 ms. That does not make the whole graph free, but it does support the cost ranking: full CocoIndex rebuild > full graph rebuild > graph scoped update. [SOURCE: `.opencode/skills/mcp-coco-index/references/tool_reference.md:80-104`] [SOURCE: `.opencode/skills/mcp-coco-index/SKILL.md:278-306`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-041.md:19-20`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-038.md:174-178`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:60:   The graph packet already rejects the idea that every query should synchronously trigger repo-wide refresh, and CocoIndex's own docs warn about concurrent `refresh_index=true` requests. Together those point away from a strict "update both indexes atomically before answering anything" design. The better model is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:63:   - enqueue semantic refresh work for CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:72:   This is the smallest design that aligns with the packet's current decisions. The research summary already says graph-specific incremental updates remain independent of CocoIndex. The code graph API work already insists on freshness metadata, stale-result warnings, and explicit maintenance surfaces. And the architectural synthesis already treats graph absence or staleness as a graceful degradation path, not a system-wide failure. So the MVP answer to this entire topic is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:74:   - independent CocoIndex refresh cycle
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:84:- Local CocoIndex command and refresh behavior:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:125:1. Keep CocoIndex and code graph refresh cycles fully independent in v1.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:128:4. Use `chokidar` plus content-hash guards plus Git reconciliation for the code graph; do not depend on CocoIndex internals for change detection.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-051.md:132:8. Prefer scoped graph repair first because it is cheaper; reserve heavy CocoIndex refreshes for semantic queries, major repo churn, or explicit repair requests.
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-config.json:2:  "topic": "Tool routing enforcement — fixing root cause of AI tool misjudgment for CocoIndex and Code Graph across hook-compatible and non-hook CLIs",
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/tasks.md:415:#### T101: Fix Missing await in memory_search
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/tasks.md:419:- **Description:** `formatSearchResults()` is async but called without await, returning Promises in `memory_search`.
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/tasks.md:444:  - `memory_search` returns fully resolved results
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-069.md:83:| 2 | Enrichment skips for non-graph tools | Call `memory_search` | No graph context appended |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-069.md:124:| T2 (instruction-file) | Verify CODEX.md / CLAUDE.md contain correct trigger instructions | Static file content assertion (grep for `memory_context` call patterns) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-069.md:125:| T3 (commands) | Test `/spec_kit:resume` YAML parsing and dispatch | Mock command executor, verify `memory_context` call shape |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-069.md:126:| T4 (Gate 1) | Test `memory_match_triggers` handler with prompt input | Standard handler test with mock DB |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-069.md:193:  it('CocoIndex seeds resolve through code graph', async () => {
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-069.md:194:    // 1. Mock CocoIndex search result with file + range
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-state.jsonl:1:{"type":"config","topic":"Tool routing enforcement — fixing root cause of AI tool misjudgment for CocoIndex and Code Graph across hook-compatible and non-hook CLIs","maxIterations":10,"convergenceThreshold":0.05,"createdAt":"2026-04-01T07:21:00.000Z","specFolder":".opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement"}
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-state.jsonl:3:{"type": "iteration", "run": 1, "status": "complete", "focus": "Map the current tool selection decision path \u2014 trace how an AI session receives tool information from MCP server instructions, PrimePackage, tool descriptions, and instruction files", "findingsCount": 7, "newInfoRatio": 0.78, "keyQuestions": ["Q1: What is the exact decision path an AI takes when choosing between Grep/Glob vs CocoIndex vs Code Graph for a search task?", "Q2: Where in the MCP server can tool-routing rules be injected so ALL CLIs receive them (not just hook-compatible ones)?", "Q3: What does buildServerInstructions() currently return and how can it be extended with routing rules under 200 tokens?"], "answeredQuestions": ["Q1: What is the exact decision path an AI takes when choosing between Grep/Glob vs CocoIndex vs Code Graph for a search task?", "Q2: Where in the MCP server can tool-routing rules be injected so ALL CLIs receive them (not just hook-compatible ones)?", "Q3: What does buildServerInstructions() currently return and how can it be extended with routing rules under 200 tokens?"], "timestamp": "2026-04-01T07:28:25.968865Z", "durationMs": 346761, "segment": 1, "noveltyJustification": "Mapped a previously undocumented split between pre-selection routing surfaces (runtime docs, server instructions, tool descriptions) and post-selection correction surfaces (PrimePackage/result hints), and confirmed that CocoIndex lives on a separate MCP provider.", "focusTrack": "routing-surfaces", "ruledOut": [{"approach": "Use PrimePackage as the main universal routing enforcement layer", "reason": "PrimePackage is injected only after the first successful tool response, so it cannot correct the initial misroute.", "evidence": "context-server.ts:834-835; hooks/memory-surface.ts:366-385"}, {"approach": "Use tool-schemas.ts alone to steer both Code Graph and CocoIndex selection", "reason": "tool-schemas.ts only defines this MCP server's tools; CocoIndex is provided by a separate provider in opencode.json.", "evidence": "context-server.ts:685-687; tool-schemas.ts:637-693; opencode.json:40-49"}]}
.opencode/specs/system-spec-kit/024-compact-code-graph/025-tool-routing-enforcement/research/deep-research-state.jsonl:4:{"type":"iteration","run":3,"status":"complete","focus":"Analyze query classification patterns that distinguish semantic discovery, structural navigation, and exact-text/path lookup, then design a lightweight classifier for routing hints","findingsCount":7,"newInfoRatio":0.46,"keyQuestions":["Q5: What patterns in user queries reliably distinguish semantic searches (CocoIndex) from structural queries (Code Graph) from exact text searches (Grep)?","Q9: How effective are tool description changes vs server instruction changes vs response hints at influencing AI tool selection?"],"answeredQuestions":["Q5: What patterns in user queries reliably distinguish semantic searches (CocoIndex) from structural queries (Code Graph) from exact text searches (Grep)?","Q9: How effective are tool description changes vs server instruction changes vs response hints at influencing AI tool selection?"],"timestamp":"2026-04-01T08:05:00.000Z","durationMs":960000,"segment":1,"focusTrack":"query-classification","noveltyJustification":"The main new insight is that the codebase already has a structural-vs-semantic heuristic, but the missing enforcement piece is a high-precision exact-text/path layer that should run before that classifier.","ruledOut":[{"approach":"Replace the existing structural-vs-semantic classifier with a heavyweight model-based router","reason":"The current heuristic is already close to sufficient if extended with an exact-text/path layer and conservative precedence rules.","evidence":"lib/code-graph/query-intent-classifier.ts:118-179"},{"approach":"Use response hints as the main routing enforcement surface","reason":"Hints are injected only after a tool call succeeds, so they can recover from a misroute but cannot prevent the initial wrong choice.","evidence":"context-server.ts:833-839"}]}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-010.md:23:| **D. Enhance CocoIndex Code** | Builds on existing, already MCP-integrated | Different approach (embeddings vs graph), limited structural awareness | Medium (1-2 weeks) | Low | 7/10 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:4:Verify whether the seven Q16 claims recorded in iterations 059 and 063 are present in the current implementation of `seed-resolver.ts`, `code-graph-db.ts`, `code-graph-context.ts`, and CocoIndex MCP registration/wrappers.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:21:### 2. Claim: CocoIndex score propagation via blended confidence `resolution * 0.6 + coco * 0.4`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:24:`resolveCocoIndexSeed()` discards the CocoIndex `score` field. It converts the seed into a plain `{ filePath, startLine, endLine }` structure and delegates to `resolveSeed()`. As a result, final confidence comes entirely from the structural resolution tier and never blends in CocoIndex relevance.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:51:`code_graph_context` supports three **graph expansion modes**: `neighborhood`, `outline`, and `impact`. It accepts precomputed seeds, including CocoIndex-originated seeds, then performs structural graph expansion only. It does not run CocoIndex searches internally, perform structural-first semantic enrichment, or execute dual-query merge logic. Those patterns remain research/design proposals rather than implemented behavior.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:58:### 6. Claim: CocoIndex MCP exposes only `search`; all management is via Spec Kit Memory wrappers
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:61:The native CocoIndex MCP server registered in `.mcp.json` runs `ccc mcp`. The CocoIndex skill documentation states that this MCP server exposes only one tool, `search`; `status`, `index`, and `reset` remain CLI-only. In this repository, management capabilities are surfaced to MCP consumers via the Spec Kit Memory wrappers `ccc_status`, `ccc_reindex`, and `ccc_feedback`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:63:Nuance: management still exists via CLI outside MCP, so the precise verified statement is: **for MCP consumers in this repo, management flows through the Spec Kit Memory wrappers rather than the native CocoIndex MCP server.**
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:93:- **Confirmed:** 1 (`search`-only native CocoIndex MCP, with management exposed through wrappers)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:103:- Inferring hybrid CocoIndex + graph search execution from seed acceptance alone
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-079.md:128:- What worked and why: Reading the live implementation files in the exact resolution/data-flow order (`seed-resolver.ts` -> `code-graph-context.ts` -> `code-graph-db.ts` -> scan/wrapper/tool registration) made it straightforward to separate **implemented behavior** from **research proposals**. The wrapper/tool-schema cross-check was especially important for claim 6, where the native CocoIndex MCP and Spec Kit Memory wrapper layer differ.
.opencode/specs/system-spec-kit/024-compact-code-graph/021-cross-runtime-instruction-parity/implementation-summary.md:88:1. Calls `session_resume()` to recover prior session state plus graph and CocoIndex availability
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:10:The public contract is intentionally low-level plus one smart entry point. `memory_context` is the documented L1 "start here" tool, `memory_match_triggers` is the fast per-turn helper, and `code_graph_status`, `code_graph_context`, and `ccc_status` are separate structural/semantic checks. [SOURCE: `tool-schemas.ts:40-43,210-212,655-698`; `README.md:509-517,605-616,1367-1372`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:12:Resume is already partially orchestrated, but only inside `memory_context`. `mode: "resume"` delegates to `handleMemorySearch` with anchors like `state`, `next-steps`, `summary`, and `blockers`, then may inject working-memory prompt context for a trusted resumed session. [SOURCE: `handlers/memory-context.ts:726-757,1291-1311`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:14:Hooked runtimes already hide some of the complexity. Startup/session-prime tells the client to call `memory_context(...resume...)` and separately warns about stale code graph state; the compaction hook already does a 3-source merge of session state, code-graph hints, and CocoIndex guidance. Non-hook CLIs do not get that automation. [SOURCE: `hooks/claude/session-prime.ts:84-120`; `hooks/claude/compact-inject.ts:166-249`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:20:| Resume baseline | `memory_context(resume)` + `code_graph_status` + `ccc_status` | ~4k+ tokens ceiling |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:21:| Resume with prompt priming | Above + `memory_match_triggers` | ~7.5k+ tokens ceiling |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:22:| Pre-task setup | `memory_match_triggers` + `memory_context` + `code_graph_context` + `task_preflight` | ~9.4k ceiling |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:36:- Description: A single tool that internally runs `memory_context({ mode: "resume", profile: "resume" })`, `code_graph_status()`, and `ccc_status()`, then returns one merged "resume packet" with session state, graph health, semantic-search readiness, and next actions.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:46:- Description: A single tool that classifies the query, chooses the best retrieval path, optionally calls `memory_context`, optionally augments with `code_graph_context`, optionally checks `ccc_status`, and returns a merged context brief rather than raw parallel tool outputs.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:50:- Risk: MEDIUM — high value, but it can easily duplicate routing logic that already exists in `memory_context` and in hook-time merge code
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:56:- Description: A kickoff tool for implementation work that runs `memory_match_triggers(prompt)`, `memory_context(input)`, and `code_graph_context(...)` for relevant files/symbols, with optional `task_preflight(...)` when the caller supplies task/spec scoring inputs.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:66:- Description: A configurable macro tool or pipeline system where users define custom step chains, such as "resume = memory_context -> code_graph_status -> ccc_status," and the server executes/merges them.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:84:| Claude/OpenCode with hooks | Hook priming + `memory_context(resume)`; graph/Coco checks partly surfaced separately | `session_resume` becomes optional convenience or hook target | Small to medium |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-101.md:85:| Copilot CLI | Manual `memory_context(resume)` + `code_graph_status` + `ccc_status` + sometimes `memory_match_triggers` | One `session_resume` call | Large |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-028.md:4:Audit all runtime agent definition files under `.claude/agents/`, `.opencode/agents/`, `.codex/agents/`, and `.gemini/agents/` for references to compaction, compact, context recovery, resume, `memory_context`, `memory_match_triggers`, and related conditional behavior, then identify the minimal hook-aware update surface.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-028.md:8:2. The current recovery instructions are resume-centric, not hook-aware. `@orchestrate` routes both known-spec and unknown interrupted work to `/spec_kit:resume`; `@handover` says `/spec_kit:resume` loads the `handover.md` this agent creates; `@speckit` exposes `memory_context(..., mode: "resume")` as session recovery and documents `/spec_kit:resume` as both "Resume existing spec" and "Resume or recover spec work." None of those instructions branch on hook output or mention a hook payload contract. [SOURCE: .opencode/agents/orchestrate.md:603-605] [SOURCE: .opencode/agents/orchestrate.md:784-788] [SOURCE: .opencode/agents/handover.md:302-306] [SOURCE: .opencode/agents/speckit.md:162-170] [SOURCE: .opencode/agents/speckit.md:551-560]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-028.md:11:5. `memory_context` and `memory_match_triggers` are already widespread, but `autoSurface` does not appear anywhere in the scanned agent files. `@context` has the densest usage and explicitly defines `memory_match_triggers -> memory_context -> memory_search` as the first retrieval layer; `@ultra-think` uses the same pair during PREPARE; `@speckit` documents `memory_context` plus its `resume` mode; `@deep-research` and `@deep-review` list `memory_context` as a tool; the remaining leaf agents only mention `memory_context`/`memory_match_triggers` in the Context Package bypass clause. No agent file contains `autoSurface`, so there is no existing always-surface agent behavior to retrofit. [SOURCE: .opencode/agents/context.md:45-50] [SOURCE: .opencode/agents/context.md:67-69] [SOURCE: .opencode/agents/context.md:117-139] [SOURCE: .opencode/agents/ultra-think.md:52-55] [SOURCE: .opencode/agents/ultra-think.md:83-89] [SOURCE: .opencode/agents/speckit.md:160-170] [SOURCE: .opencode/agents/deep-research.md:233-236] [SOURCE: .opencode/agents/deep-review.md:282-285]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-028.md:14:8. The minimal diff is small and mechanical: add one hook-awareness branch to the existing Context Package or memory-entry preamble in the affected agents, not a full workflow rewrite. In practice that means: `@context` changes from unconditional memory-first to "hook payload first when present and sufficient, else current memory-first"; `@orchestrate` invalidates its agent-definition reuse shortcut when compaction has occurred and forwards the hook payload as part of the Context Package; `@handover`, `@speckit`, `@review`, `@write`, `@debug`, and `@ultra-think` reuse their existing "If dispatched with a Context Package..." branch, but extend it to explicitly accept a hook-produced recovery bundle. `@deep-research` only needs a short note to consume hook-supplied context before calling `memory_context`; `@deep-review` likely needs no behavioral change beyond optional terminology clarification to avoid confusing `compact skeptic/referee` with context compaction. [SOURCE: .opencode/agents/context.md:45-50] [SOURCE: .opencode/agents/context.md:117-139] [SOURCE: .opencode/agents/orchestrate.md:155-162] [SOURCE: .opencode/agents/handover.md:99-103] [SOURCE: .opencode/agents/speckit.md:121-123] [SOURCE: .opencode/agents/review.md:60-64] [SOURCE: .opencode/agents/write.md:83-87] [SOURCE: .opencode/agents/debug.md:95-99] [SOURCE: .opencode/agents/ultra-think.md:52-55] [SOURCE: .opencode/agents/deep-research.md:233-236] [SOURCE: .opencode/agents/deep-review.md:138-141] [SOURCE: .opencode/agents/deep-review.md:386-388]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-028.md:19:- Context or memory API hits: all 10 files in each populated runtime reference `memory_context`, `memory_match_triggers`, or a Context Package branch.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-028.md:37:- Fall back to `memory_match_triggers` / `memory_context` only for missing fields.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-028.md:44:4. In `@context`, replace the unconditional `memory_match_triggers -> memory_context -> memory_search` preamble with a hook-first preamble that only drops into Layer 1 when the hook payload is absent or insufficient. [SOURCE: .opencode/agents/context.md:45-50] [SOURCE: .opencode/agents/context.md:117-139]
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/implementation-summary.md:26:The most critical discovery was a missing `await` on `formatSearchResults()` calls in the MCP server, causing `memory_search` to return Promise objects instead of actual results when `includeContent=true` - a production-breaking bug affecting core functionality. Other critical issues included an entirely unused config system, a non-functional ANCHOR system with false "93% token savings" claims, undefined error codes, and missing rate limiting for embedding API calls.
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/spec.md:83:**Problem:** When you start a session in Codex CLI or Copilot CLI, you get nothing — no memory, no code graph status, no prior work context. You have to manually call `memory_context` every time. Claude Code users get all this automatically via hooks.
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/spec.md:95:- CocoIndex availability
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/spec.md:114:- **stale** — probable context loss (should call `memory_context` to recover)
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/spec.md:161:| F046 CocoIndex path fix | DONE | Prime package uses isCocoIndexAvailable() helper instead of process.cwd()-based lookup |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/007-hook-parity/003-codex-native-startup-advisor-hooks/implementation-summary.md:121:2. **CocoIndex timed out during implementation.** Code exploration used direct file reads and `rg` after semantic search timed out.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-008.md:75:| Context pre-loading | CocoIndex only | CocoIndex + structural ranking |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:4:Investigate GitHub Copilot CLI's real instruction-loading surface and use it to design a reliable non-hook startup pattern for `memory_context` and `code_graph_scan`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:12:5. Design session-start auto-trigger patterns for `memory_context` and `code_graph_scan`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:29:- a research/exploration workflow that starts with `memory_match_triggers()` and then `memory_context()` / `memory_search()`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:30:- Gate 1 instructions that explicitly require `memory_match_triggers(prompt)` at turn start
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:42:- after compaction: call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:44:- on session start: rely on `memory_match_triggers()` plus hook-based priming when available
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:48:- keep `memory_match_triggers(prompt)` as the universal first-turn behavior
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:49:- if the first turn implies resume / continue / compaction / clear / prior work, immediately call `memory_context(... profile: "resume")`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:77:1. Call `memory_match_triggers(prompt)`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:79:   `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:96:- semantic discovery ("where is X implemented?") -> stay CocoIndex-first, then use code graph secondarily
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-086.md:98:This aligns with the repo's existing `AGENTS.md` rule that semantic code discovery should be CocoIndex-first while structural navigation should use code graph tools.
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/checklist.md:81:- [x] Budget allocator enforces floors (constitutional 700, graph 1200, CocoIndex 900, triggered 400) [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/checklist.md:87:- [x] Graceful degradation: if Code Graph or CocoIndex unavailable, remaining sources fill budget [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/continuation-prompt.md:65:### Phase 012 — CocoIndex UX (1 item)
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/continuation-prompt.md:69:9. `[ ] Agent routing tests validate CocoIndex-first behavior`
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/continuation-prompt.md:71:   - Test that `@context` agent configuration prioritizes CocoIndex for semantic queries
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/continuation-prompt.md:72:   - Verify routing: semantic intent → CocoIndex, structural → code_graph, session → memory
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/continuation-prompt.md:133:- `seed-resolver.ts` — CocoIndex → graph node resolution
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/continuation-prompt.md:142:- `ccc-status.ts`, `ccc-reindex.ts`, `ccc-feedback.ts` — 3 CocoIndex tools
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:1:# Iteration 59: CocoIndex Utilization Improvements (Q16)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:4:Investigate how CocoIndex utilization can be improved across four dimensions: (1) automatic re-indexing triggers, (2) smarter seed resolution in seed-resolver.ts, (3) query routing between structural (code graph) and semantic (CocoIndex) search, and (4) hybrid query patterns combining both systems for better results.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:12:**A. Fuzzy line matching is absent.** The exact match (`start_line = ?`) fails when CocoIndex chunk boundaries don't align perfectly with symbol start lines. CocoIndex's RecursiveSplitter uses 1000-char chunks with 150-char overlap, so chunk start lines often land mid-function rather than at the function declaration. A range-overlap query (`WHERE start_line <= ? AND end_line >= ?`) already exists as the "enclosing" fallback, but it's only tried after exact fails. A better approach: combine exact + near-exact (within N lines) before falling through to enclosing.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:21:This would match when CocoIndex reports line 45 but the function starts at line 43. Confidence: 0.95 (between exact's 1.0 and enclosing's 0.7).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:29:**C. No score propagation from CocoIndex.** `resolveCocoIndexSeed()` discards the CocoIndex similarity score entirely -- it converts to a bare `CodeGraphSeed` and delegates. The original CocoIndex score could inform the confidence value of the `ArtifactRef`, especially when combined with resolution quality. A seed with CocoIndex score 0.9 + enclosing resolution should have higher confidence than one with CocoIndex score 0.3 + enclosing resolution.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:35:Currently, CocoIndex re-indexing is fully manual (`ccc index` CLI or `ccc_reindex` MCP tool). The daemon architecture supports background indexing, but no automatic triggers exist. Three trigger points are viable:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:37:**A. On branch switch (git checkout/switch).** Branch switches are the highest-impact change event because they can modify hundreds of files at once. Detection approach: watch for `.git/HEAD` changes via file watcher, or intercept `git` commands via shell hooks. CocoIndex already handles file-level diffing during indexing, so a branch-switch trigger just needs to invoke `ccc index` (incremental). The code graph (`code_graph_scan`) already has incremental indexing via content hash -- coordinating both is the key challenge.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:39:**B. On session start.** The CocoIndex SKILL.md already mandates "ALWAYS check index status before searching" and "suggest reindexing if codebase has changed significantly." This could be automated: during SessionStart hook (or equivalent), check `ccc status` and auto-trigger `ccc index` if stale. The daemon's auto-restart on version mismatch shows this pattern already exists partially.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:41:**C. On file save (debounced).** Individual file saves are low-impact but frequent. A debounced trigger (e.g., 30 seconds after last save) would keep both indexes fresh. The code graph's `code_graph_scan` already supports incremental indexing with content hash checks, making individual file updates cheap. CocoIndex's daemon architecture supports background indexing and "search during indexing" (streams IndexWaitingNotice), so freshness wouldn't block searches.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:50:**A. Keyword-based pre-classification.** The CocoIndex SKILL.md already has intent signals with weighted scoring (SEARCH: weight 4, INDEX: weight 4, etc.). This pattern can be generalized to route between CocoIndex semantic search and code graph structural queries:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:55:| "find code that does X", "implementations of" | CocoIndex (search) | Semantic/intent query |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:57:| "how is X implemented" | Both (CocoIndex -> Code Graph) | Start semantic, expand structural |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:60:**B. Confidence-based fallback routing.** When CocoIndex returns low-similarity results (all below 0.3), automatically fall back to code graph structural search. When code graph returns file_anchor resolution (no symbol match), suggest CocoIndex semantic search for better results.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:67:### 4. Hybrid Query Patterns: CocoIndex Seeds into Code Graph Expansion
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:69:The current architecture already supports CocoIndex -> Code Graph bridging via `CocoIndexSeed` type in seed-resolver.ts. But the pattern is one-directional. Three hybrid patterns would improve results:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:71:**A. Structural expansion of semantic results.** After CocoIndex finds semantically relevant code, automatically expand via code graph to include callers, callees, and imported modules. This is already supported via `code_graph_context` with `queryMode: 'neighborhood'`, but the AI must explicitly chain the calls. An integrated `hybrid_search` tool could automate: CocoIndex search -> resolve seeds -> expand neighborhood -> merge into single response.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:73:**B. Semantic enrichment of structural results.** After code graph returns a call chain or dependency tree, use CocoIndex to find semantically similar code that isn't structurally connected. Example: after finding all callers of `resolveSeed()`, CocoIndex could find other resolution/lookup patterns in the codebase that use similar logic but aren't in the call graph.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:75:**C. Working set warm-up.** On session start, use the code graph to identify the "hot" files from the last session (files with recent edits tracked via `code_files.indexed_at`), then use CocoIndex to pre-fetch semantically adjacent code. This creates a broader initial context than either system alone.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:78:[SOURCE: /Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/seed-resolver.ts:18-25 (CocoIndexSeed type)]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:80:### 5. Underutilized CocoIndex Features
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:82:Analysis of the CocoIndex MCP skill reveals several capabilities not fully leveraged by the current integration:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:84:**A. Language and path filters are not passed through.** The CocoIndex `search` tool accepts `languages` (list) and `paths` (list) filter parameters, but the seed-resolver and code-graph-context modules don't pass these through when initiating CocoIndex searches. Using code graph file metadata (language column in `code_nodes`) to auto-filter CocoIndex searches by relevant language would improve precision.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:86:**B. `refresh_index` parameter management.** The skill documents a known concurrency issue: simultaneous `refresh_index=true` requests cause `ComponentContext` errors. The integration should track whether a refresh has occurred in the current session and automatically set `refresh_index=false` for subsequent calls. The `computeFreshness()` function in code-graph-context.ts already tracks staleness -- this could be extended to CocoIndex freshness.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:88:**C. `ccc_feedback` tool is available but never called.** The Spec Kit Memory MCP exposes `ccc_feedback` for submitting search result quality feedback, but no code path automatically calls it. After the AI uses a CocoIndex result (e.g., reads the file, uses the finding), implicit positive feedback could be logged. This would build a quality signal over time.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:95:- **Real-time file watcher for CocoIndex re-indexing**: Too complex for the current architecture. The daemon already handles background indexing; adding another file watcher creates duplicate infrastructure and coordination complexity. Debounced session-level triggers are sufficient.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-059.md:115:- What worked and why: Direct file analysis of both seed-resolver.ts and code-graph-context.ts alongside the CocoIndex SKILL.md revealed concrete improvement opportunities that wouldn't be visible from external documentation alone. The code shows exact gaps (missing near-exact matching, discarded CocoIndex scores, no auto-filter passthrough).
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/tasks.md:70:- [x] Implement `budget-allocator.ts` with floor allocations (constitutional 700, graph 1200, CocoIndex 900, triggered 400), overflow pool computation, priority-order redistribution, and deterministic trim order — lib/code-graph/budget-allocator.ts
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/tasks.md:80:- [x] Graceful degradation when Code Graph or CocoIndex unavailable — remaining sources fill budget
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-075.md:17:| Q16: CocoIndex utilization | 059, 063 | Fully answered | Near-exact seed resolution + auto-reindex triggers + hybrid query patterns |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-075.md:31:| 5 | 046-055 | GPT-5.4 parallel agents | CocoIndex integration | Bridge, budget allocator, intent router |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-075.md:40:1. **Architectural Decision Record**: Reject Dual-Graph, build clean-room code graph + hook architecture + CocoIndex integration. Evidence: 10 iterations of evaluation, 5 hard blockers identified.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-075.md:44:3. **Technical Reference**: Detailed API contracts (autoSurfaceAtCompaction, memory_context resume flow, code_graph_context seeds), hook schemas (PreCompact/SessionStart/Stop), performance constraints (1800ms budget, SQLite <10ms, CocoIndex 100-500ms), error recovery (4-level degradation), testing strategy (6 test files, 40 cases).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-075.md:54:| CocoIndex `refresh_index` concurrent request handling | Low | Known issue (ComponentContext errors), needs CocoIndex-side fix |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-075.md:55:| ccc_feedback implicit positive feedback implementation | Low | Design trivial, value uncertain until CocoIndex usage matures |
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:79:Improve CocoIndex integration (seed resolution, query-intent metadata, auto-reindex) and update instruction files across all 5 runtimes to auto-trigger code graph + memory context on session start. Consolidate recovery documentation.
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:98:- CocoIndex score propagation: blended confidence `resolution * 0.6 + coco * 0.4`
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:120:- **AGENTS.md**: Add Session Start Protocol section — force `memory_context()` + `code_graph_status()` on first turn
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:168:| 39: Near-exact seeds | **PARTIAL** | +/-5 lines, graduated confidence, composite index complete; CocoIndex score blending deferred |
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:184:2. Route: structural keywords → code_graph_query, semantic → CocoIndex search
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:190:### CocoIndex Score Propagation
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:191:**Status:** DEFERRED — requires CocoIndex API integration
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:192:**Dependency:** CocoIndex MCP server needs to expose a relevance scoring endpoint
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/spec.md:194:1. Expose semantic relevance scores from CocoIndex search responses
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/plan.md:84:   - Route: structural → code_graph_query, semantic → CocoIndex search, ambiguous → both
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/plan.md:118:- Verify intent routing: "what calls functionX" → code graph, "find similar to X" → CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-024.md:12:1. `COMPACTION_TOKEN_BUDGET` is a fixed hook-level constant, not a dynamic setting. It is defined as `4000` in `memory-surface.ts`, documented as the compaction hook max, exported from the module, and passed directly into `autoSurfaceMemories(..., COMPACTION_TOKEN_BUDGET, 'compaction')` by `autoSurfaceAtCompaction()`. The compaction path is invoked from `context-server.ts` specifically when `memory_context` runs in `resume` mode. Sources: `mcp_server/hooks/memory-surface.ts:52-55`, `mcp_server/hooks/memory-surface.ts:283-316`, `mcp_server/hooks/memory-surface.ts:323-336`, `mcp_server/context-server.ts:325-339`.
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/implementation-orchestration-prompt.md:310:2. **`profile: "resume"` required** — without it, `memory_context(resume)` returns search results not a brief
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:141:**Most Critical Discovery (NEW):** Missing `await` on `formatSearchResults()` in context-server.js (lines 1085, 1140, 1161) causes `memory_search` to return Promise objects instead of actual results when `includeContent=true`. **This is a production bug that breaks core functionality.**
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:407:        BREAKS memory_search when includeContent=true
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:785:resume.md:435 - Double prefix: "spec_kit_memory_memory_search"
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:786:Should be: "memory_search" or "spec_kit_memory_search"
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:800:research/research.md:107-109 - memory_match_triggers() no error handling
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:897:- memory_search schema mismatch
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:1150:**Issue 10.2: memory_search Required Param Not Emphasized**
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/064-bug-analysis-and-fix/research/research.md:1317:1. **Why** does memory_search return Promise objects?
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/implementation-summary.md:70:The compaction pipeline now merges three sources (constitutional/triggered memory, structural code graph, CocoIndex semantic neighbors) through a budget-aware allocator instead of the previous Memory-only path. A session working-set tracker seeds graph expansion and semantic search at compaction time.
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/implementation-summary.md:74:`working-set-tracker.ts` maintains a per-session record of files and symbols accessed during the conversation. Each entry tracks access count and last-access timestamp. `getTopRoots(n)` returns the top-N entries weighted by recency and frequency, used to seed `code_graph_context(queryMode: 'neighborhood')` and CocoIndex semantic queries at compaction time. Symbol-level tracking is supported via `trackSymbol()`.
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/implementation-summary.md:78:`budget-allocator.ts` accepts a total token budget (default 4000, also supports 1500/2500) and per-source payload sizes. Floor allocations are enforced: constitutional 700, graph 1200, CocoIndex 900, triggered 400, overflow pool 800. When a source returns empty or under its floor, the unused tokens flow to the overflow pool and are redistributed to the highest-priority sources that can use more. When the total exceeds budget, a deterministic trim order is applied: semantic tail first, then graph leaves, triggered memories, direct neighbors, state/next-steps, and constitutional last (never dropped). Returns an `AllocationResult` with per-source granted budgets, dropped item counts, and redistribution metadata.
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/implementation-summary.md:118:| Zero-budget sections suppressed | Rendering an empty "Semantic Neighbors" header when CocoIndex is unavailable wastes tokens and confuses the AI. |
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/implementation-summary.md:129:| CocoIndex empty: overflow redistribution correct | Verified |
.opencode/specs/system-spec-kit/024-compact-code-graph/011-compaction-working-set/implementation-summary.md:140:1. **Code graph and CocoIndex sources are placeholder text.** The current output renders placeholder content for structural and semantic sections instead of real retrieval results.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:17:OpenCode/Copilot delegates first turn to `@context-prime`, which does `memory_context` + `code_graph_status` + `ccc_status` + `session_health` and returns a compact Prime Package (`.opencode/agents/context-prime.md:34-41`).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:20:`primeSessionIfNeeded()` runs before tool dispatch, sets `sessionPrimed`, and injects constitutional memories, code-graph status, and a `primePackage` with `specFolder`, `currentTask`, graph freshness, CocoIndex availability, and recommended next calls (`hooks/memory-surface.ts:315-420`, `context-server.ts:707-715,530-565`).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:23:`session_resume()` returns memory + code graph + CocoIndex + hints (`handlers/session-resume.ts:45-127`), and `session_health()` reports priming status, graph freshness, inactivity, and hints (`handlers/session-health.ts:50-136`).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:52:| First call not memory-related | `primePackage` is derived only from args like `input/query/prompt/specFolder`; weak first calls produce `null` task/spec and recommend `memory_context(...)` (`memory-surface.ts:320-360`) | Need deterministic tests for "context-free first call" |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:82:  - `@context-prime` requires `memory_context`, `code_graph_status`, `ccc_status`, `session_health`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:83:  - `opencode.json` wires Spec Kit Memory and CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:106:- context-free first call produces `recommendedCalls` including `memory_context(...)`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:122:- assert Prime Package contains spec/task/graph/CocoIndex info
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:140:- disable hooks and confirm root recovery protocol still works with `session_resume()` or `memory_context + code_graph_status`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:150:- first-turn Session Start Protocol: `session_resume()` or `memory_context + code_graph_status`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-109.md:232:- it already composes memory, code graph, and CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:1:# Iteration 055: Implementation Readiness Assessment — CocoIndex-Aware Code Graph Architecture
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:18:   6. Implement Phase 010 `code_graph_context` and CocoIndex-seed resolution.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:38:     - CocoIndex seed normalization and span-to-node resolution
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:42:     - 3-source merge: Memory + CocoIndex + Code Graph
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:61:   - CocoIndex-seed bridge model
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:70:   - seed-to-node resolution accuracy for CocoIndex spans
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:85:   CocoIndex bridge MVP:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:104:   - seed-to-node ambiguity for CocoIndex spans
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:157:   CocoIndex remains external and independent; the code graph stays integrated.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:186:   | Phase 010 `code_graph_context` + CocoIndex bridge | 3 | Strong design, but seed-resolution quality still needs proof |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-055.md:200:- Decision-level contract for CocoIndex vs code graph and phases 008+:
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/checklist.md:128:- [x] Query routing decision tree documented (structural→code_graph, semantic→CocoIndex, session→Memory) [EVIDENCE: line 779]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:1:# Iteration 049: Token Budget Allocation Across Memory + CocoIndex + Code Graph
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:8:2. CocoIndex semantic code retrieval
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:34:3. The best `4000`-token default is `Memory 1000 + CocoIndex 400 + Code Graph 1400 + Flex 1200`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:40:   - CocoIndex should have the smallest floor because DR-010 and later iterations consistently treat it as the semantic recall/seed layer, not the main payload layer.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:48:   - CocoIndex floor: `400`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:55:   - CocoIndex `10%`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:68:   2. Run CocoIndex to collect semantic seeds.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:69:   3. Expand Code Graph from active symbols/files plus the top CocoIndex seeds.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:88:   - if CocoIndex returns no trustworthy seeds, move its `400` floor to flex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:102:   This matches the packet's "cut breadth before depth" guidance and the recommendation to use CocoIndex as a bounded semantic boost, not as the primary definition of the working set. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:92-102`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:31-41`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:101-132`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:145:2. CocoIndex should seed structural expansion rather than replace it,
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:162:   - CocoIndex `400`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-049.md:167:   - CocoIndex seeds
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/tasks.md:70:- [x] Create feature catalog entries for PreCompact Hook, SessionStart Priming, Stop Token Tracking, Cross-Runtime Fallback, Runtime Detection, CocoIndex Integration — entries in `.opencode/skills/system-spec-kit/feature_catalog/`
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/tasks.md:73:- [x] Update `.opencode/skills/system-spec-kit/SKILL.md` with Code Graph section — CocoIndex (semantic) + Code Graph (structural) + Memory (session) complementary architecture
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/tasks.md:106:- [x] **Step 3b**: Expand `../../../../skill/system-spec-kit/SKILL.md` Code Graph section — edge types, auto-trigger, query routing, CCC tools, session tools, CocoIndex seed resolution
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/tasks.md:79:- [x] F046 fixed — CocoIndex availability now uses the shared helper instead of process.cwd()-based lookup
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-061.md:37:The `extractContextHint` function (memory-surface.ts:67-84) checks args for fields `['input', 'query', 'prompt', 'specFolder', 'filePath']` in that priority order, returning the first string >= 3 chars. For code graph auto-enrichment, the `filePath` field is the primary signal. However, `extractContextHint` returns the **first match**, which for memory_context calls would be `input` (a query string), not `filePath`. A dedicated `extractFilePathHint(args)` function should be created for graph enrichment that specifically looks for file-path-shaped arguments:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-061.md:143:3. Similarly check CocoIndex staleness and trigger `handleCccReindex({ full: false })`
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/implementation-summary.md:83:| CocoIndex Integration | Context Enrichment | Semantic code search complementing structural code graph and memory context |
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/implementation-summary.md:91:During the original Phase 006 delivery, `.opencode/skills/system-spec-kit/SKILL.md` received two new sections: a Hook System section documenting the lifecycle (PreCompact -> cache -> SessionStart -> inject), registration in `.claude/settings.local.json`, hook script locations and compilation, and the design principle that hooks are transport mechanisms rather than separate business logic. A Code Graph section documents the complementary architecture where CocoIndex handles semantic search, Code Graph handles structural navigation, and Memory handles session continuity.
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/implementation-summary.md:112:- `.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md` plus the category-07 integration scenarios now test the current semantic-path, graph-augmentation, and CocoIndex availability semantics instead of older daemon-liveness / merged-result assumptions.
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/implementation-summary.md:127:| `.opencode/skills/system-spec-kit/manual_testing_playbook/22--context-preservation-and-code-graph/263-session-resume.md` | Modified | Resume scenario now validates the full structural contract and current CocoIndex triage path |
.opencode/specs/system-spec-kit/024-compact-code-graph/006-documentation-alignment/implementation-summary.md:150:| Six feature catalog entries (not five) | CocoIndex Integration was added as a sixth entry to document the three-system architecture alongside the five hook-specific features. |
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/implementation-summary.md:75:When the MCP server receives its first tool call in a session, `primeSessionIfNeeded()` in `context-server.ts` gathers a `PrimePackage` containing the last active spec folder, code graph freshness status, CocoIndex availability, and recommended next calls. This is injected as structured meta + human-readable hints into the tool response. The `enforceAutoSurfaceTokenBudget` keeps the payload bounded. A `sessionPrimed` boolean flag prevents re-priming on subsequent calls.
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/implementation-summary.md:82:- **stale** — probable context loss (should call `memory_context` to recover)
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/implementation-summary.md:107:This phase delivered the server-side pieces first: first-call auto-priming, the `session_health` handler, and the dispatch wiring needed to expose both without runtime hooks. Later fixes closed the two review findings tied to priming retry behavior and CocoIndex path detection, while leaving the remaining `session_health` signal gaps documented instead of overstating completion.
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/implementation-summary.md:115:| Close F045 and F046 in the phase record | The code now flips `sessionPrimed` after successful priming and uses `isCocoIndexAvailable()` for CocoIndex detection. |
.opencode/specs/system-spec-kit/024-compact-code-graph/018-non-hook-auto-priming/implementation-summary.md:135:5. **Previously deferred F045/F046 are now closed.** `sessionPrimed` flips after successful priming, and CocoIndex availability now uses the shared helper instead of a `process.cwd()` lookup.
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/audit-2026-04-24/findings-metadata.md:110:  - `.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/description.json:1-19 -> 1: { | 2: "specFolder": "system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context", | 3: "description": "Phase 010: CocoIndex Bridge + code_graph_context", | 4: "keywords": [ | 5: "phase", | 6: "010", | 7: "cocoindex", | 8: "bridge" | 9: ], | 10: "lastUpdated": "2026-04-13T04:56:38.124Z", | 11: "specId": "010", | 12: "folderSlug": "cocoindex-bridge-context", | 13: "parentChain": [ | 14: "system-spec-kit", | 15: "024-compact-code-graph" | 16: ], | 17: "memorySequence": 0, | 18: "memoryNameHistory": [] | 19: }`
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/audit-2026-04-24/findings-metadata.md:112:  - `.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:1-8 -> 1: <!-- SPECKIT_TEMPLATE_SOURCE: system-spec-kit templates | v2.2 --> | 2: --- | 3: title: "Implementation Summary: CocoIndex Bridge + code_graph_context [024/010]" | 4: description: "Implemented code_graph_context orchestration tool bridging CocoIndex semantic search into structural graph neighborhoods with seed resolution, three query modes, and budget-aware formatting. 22/22 checklist items verified." | 5: --- | 6: # Implementation Summary | 7:  | 8: `
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/audit-2026-04-24/findings-metadata.md:128:  - `.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/description.json:1-20 -> 1: { | 2: "specFolder": "system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization", | 3: "description": "Feature Specification: Phase 012 — CocoIndex UX, Utilization & Usefulness", | 4: "keywords": [ | 5: "feature", | 6: "specification", | 7: "phase", | 8: "012", | 9: "cocoindex", | 10: "utilization", | 11: "usefulness" | 12: ], | 13: "lastUpdated": "2026-04-13T04:56:38.506Z", | 14: "specId": "012", | 15: "folderSlug": "cocoindex-ux-utilization", | 16: "parentChain": [ | 17: "system-spec-kit", | 18: "024-compact-code-graph" | 19: ], | 20: "memorySequence": 0,`
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/audit-2026-04-24/findings-metadata.md:130:  - `.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/implementation-summary.md:1-8 -> 1: <!-- SPECKIT_TEMPLATE_SOURCE: system-spec-kit templates | v2.2 --> | 2: --- | 3: title: "Implementation Summary: Phase 012 — CocoIndex UX, Utilization & Usefulness" | 4: description: "Summarize what Phase 012 delivered, what stayed partial, and how the packet now reflects current reality." | 5: trigger_phrases: | 6: - "implementation summary" | 7: - "phase 012" | 8: - "cocoindex"`
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/audit-2026-04-24/findings-metadata.md:202:  - `.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:1-8 -> 1: <!-- SPECKIT_TEMPLATE_SOURCE: system-spec-kit templates | v2.2 --> | 2: --- | 3: title: "Implementation Summary: Query-Routing Integration [024/020]" | 4: description: "Query-intent enrichment in memory_context, slim session_resume output, and passive enrichment wired into the response path." | 5: --- | 6: # Implementation Summary | 7:  | 8: `
.opencode/specs/system-spec-kit/024-compact-code-graph/scratch/audit-2026-04-24/findings-metadata.md:337:  - `.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/implementation-summary.md:1-9 -> 1: --- | 2: title: "Implementation Summary: Code Graph Auto-Reindex Parity [005/030]" | 3: description: "Phase 005 implements bounded code graph auto-reindex parity so structural reads now behave more like CocoIndex while still refusing inline full scans." | 4: trigger_phrases: | 5: - "phase 5 implementation summary" | 6: - "auto reindex parity summary" | 7: importance_tier: "important" | 8: contextType: "implementation" | 9: ---`
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/051-lib-consolidation/verification-test-plan.md:126:    const text = 'Called generateContext and used memory_search function';
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/051-lib-consolidation/verification-test-plan.md:200:- [ ] Test: `memory_search()` executes without error
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/051-lib-consolidation/verification-test-plan.md:208:    console.log('memory_search module:', hybridSearch ? 'PASS' : 'FAIL');
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/051-lib-consolidation/verification-test-plan.md:417:| **Integration** | memory_search executes | [ ] |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:9:Claude Code has a complete 3-event lifecycle hook system (`PreCompact`, `SessionStart`, `Stop`) implemented in `hooks/claude/`. The `session-prime.ts` handler routes by source (`compact`, `startup`, `resume`, `clear`) and injects context via stdout. It includes code graph stale-index detection, CocoIndex availability checks, and 3-source merge payload injection after compaction. No other runtime has this level of integration.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:14:- **Compaction recovery**: "FIRST ACTION -- call: `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`"
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:15:- **Query-intent routing**: Explicit routing table for semantic discovery (CocoIndex), structural navigation (Code Graph), and session continuity (Memory)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:16:- **Two universal retrieval primitives**: `memory_match_triggers(prompt)` for turn-start context, `memory_context({ mode: "resume" })` for compaction recovery
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:21:The resume command provides a comprehensive 4-5 step workflow for session recovery that is completely runtime-agnostic. It uses only MCP tools (memory_context, memory_search, memory_match_triggers) -- no hooks required. Detection flow: validate path -> memory_match_triggers -> memory_context -> deterministic ranking -> user prompt. Context loading: handover.md -> memory_context(resume) -> CONTINUE_SESSION.md -> memory_search -> checklist.md. This serves as the universal "manual hook equivalent" for all runtimes.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:29:MCP servers are stateless request handlers. They cannot detect session start, compaction, or new-session events on their own. However, the `memory_context` handler already supports `mode: "resume"` which serves as a session-start detection proxy. A potential enhancement: track the timestamp of last MCP tool call per session. If the gap between calls exceeds a threshold (e.g., >5 minutes), treat the next call as a "session restart" and proactively include recovery context. This would be a server-side heuristic that works across all runtimes.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:30:[INFERENCE: based on MCP tool statelessness from hooks/README.md and memory_context handler patterns]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:38:| **T2: Instruction-file triggers** | CODEX.md / CLAUDE.md / GEMINI.md instructions telling AI to call memory_context at session start | Codex CLI, Copilot, Gemini | Good (relies on AI compliance) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:40:| **T4: Gate 1 automatic** | CLAUDE.md Gate 1 requires `memory_match_triggers()` on EACH new message | All runtimes | Basic (triggered context only, no full session recovery) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:45:OpenCode (Copilot) agent definitions in `.opencode/agents/` are functionally identical to Claude/Codex agents regarding MCP tool access. The key difference: OpenCode uses markdown agent files with YAML frontmatter and `mcpServers` arrays. It has NO hook system, so it relies entirely on T2 (CLAUDE.md instruction triggers) and T3 (/spec_kit:resume). The root CLAUDE.md serves as the universal instruction file that forces Gate 1 (memory_match_triggers) on every message.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:49:A new approach that could bridge the T1-T2 gap: implement "first-call priming" in the MCP server itself. When any MCP tool (memory_context, memory_search, code_graph_query, etc.) is called for the first time in a session (no prior calls in the last N minutes), the response could include a `_sessionPriming` metadata section with:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:50:- Constitutional memories (already surfaced by memory_context)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:52:- CocoIndex availability status
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-058.md:85:Q16 -- CocoIndex utilization improvements: automatic re-indexing triggers, smarter seed resolution from code_graph_context results, and query routing between structural graph and semantic search. This is the final remaining question for Segment 6.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:9:1. Root `CLAUDE.md` does not contain a dedicated compaction-recovery section. The only active recovery guidance is the high-level quick-reference material that says research should use memory tools and prior work should be resumed with `/spec_kit:resume` or `memory_context({ input: "resume previous work continue session", mode: "resume", specFolder })`. That matches iteration 012's conclusion that root `CLAUDE.md` has "only high-level recovery guidance, not a real post-compact playbook." [SOURCE: `CLAUDE.md:35-36`] [SOURCE: `CLAUDE.md:44-52`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:12-25`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:13:   > `| **Research/exploration**  | `memory_match_triggers()` → `memory_context()` (unified) OR `memory_search()` (targeted) → Document findings |`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:15:   > `| **Resume prior work**     | `/spec_kit:resume` OR `memory_context({ input: "resume previous work continue session", mode: "resume", specFolder })` → Review checklist → Continue |`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:17:   There is no root-level instruction that says "after compaction, immediately call resume-mode memory_context", no requirement to re-read `CLAUDE.md`, and no mention of `profile: "resume"`. [SOURCE: `CLAUDE.md:49-51`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:19-23`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:21:4. Root `CODEX.md` does not exist, so there are currently no Codex-specific recovery instructions in-repo. The packet explicitly says `CODEX.md` should be updated with compaction recovery and that runtime docs should reference the same two primitives: `memory_match_triggers` and `memory_context(resume)`. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:65-69`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:25:   - `memory_match_triggers()` in root `CLAUDE.md` research flow. [SOURCE: `CLAUDE.md:49-49`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:27:   - `memory_context({ input: "resume previous work continue session", mode: "resume", specFolder })` in root `CLAUDE.md`. [SOURCE: `CLAUDE.md:51-51`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:28:   - `memory_context({ mode: "resume", profile: "resume", input: "context compaction recovery" })` in the phase-4 proposed `CLAUDE.md` enhancement. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:47-56`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:31:6. `memory_context({ mode: "resume", profile: "resume" })` is referenced in the spec packet, but not in the live instruction files that were inspected. It appears in the decision record as a required contract for all resume paths, in the phase-4 fallback spec as the exact post-compaction call to add to `CLAUDE.md`, and in broader packet planning/checklist material. It does not appear in root `CLAUDE.md`, cannot appear in missing `.claude/CLAUDE.md` or `CODEX.md`, and does not appear in the user-global `~/.claude/CLAUDE.md`. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:69-74`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:47-56`] [SOURCE: `CLAUDE.md:44-52`] [SOURCE: `/Users/michelkerkmeester/.claude/CLAUDE.md:1-22`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:35:   - Gap A: No provider lifecycle hook. `autoSurfaceAtCompaction()` only runs when our MCP later receives `memory_context(..., mode: "resume")`; nothing fires automatically unless the AI or operator calls the resume workflow. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:135-143`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:12-12`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:43:   1. `IMMEDIATELY call memory_context({ mode: "resume", profile: "resume", input: "context compaction recovery" })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:52:   - Root `CLAUDE.md`: cross-runtime, portable recovery contract shared across assistants and sessions; it should name the canonical primitives and the exact profiled `memory_context` call. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:42-56`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:67-69`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:59:  > `| **Research/exploration**  | `memory_match_triggers()` → `memory_context()` (unified) OR `memory_search()` (targeted) → Document findings |`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:61:  > `| **Resume prior work**     | `/spec_kit:resume` OR `memory_context({ input: "resume previous work continue session", mode: "resume", specFolder })` → Review checklist → Continue |`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:85:  > `1. IMMEDIATELY call memory_context({ mode: "resume", profile: "resume", input: "context compaction recovery" })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:111:1. Update root `CLAUDE.md` with a dedicated `## Context Compaction Behavior` section that uses the exact profiled call from phase 4: `memory_context({ mode: "resume", profile: "resume", input: "context compaction recovery" })`. Do not leave recovery buried only in the quick-reference table. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:42-56`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-030.md:115:3. Add `CODEX.md` with the same cross-runtime fallback primitives as root `CLAUDE.md`: `memory_match_triggers` plus the profiled resume-mode `memory_context` call. Codex-specific content should stay tool-based because the phase-4 packet treats non-Claude runtimes as fallback consumers rather than hook-driven runtimes. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/004-cross-runtime-fallback/spec.md:65-69`]
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/051-lib-consolidation/plan.md:165:# Test memory_search via MCP
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:76:This packet drifted away from the shipped implementation. The stale docs described `memory_context` as selective backend routing, documented the wrong response metadata shape, claimed `session_resume` merged `ccc_status()`, and marked passive enrichment as deferred even though it is wired in.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:88:- Document `memory_context` as additive enrichment over the existing traced semantic flow.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:90:- Document `session_resume` as resume context + graph summary + CocoIndex availability, with the real schema and output shape.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:96:- Reintroducing selective backend dispatch from `memory_context` into `code_graph_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:103:| `handlers/memory-context.ts` | Modify | Query intent classification remains inside `memory_context`; optional graph context is appended to traced results. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:104:| `handlers/session-resume.ts` | Create | Composite resume tool returning memory context, code graph summary, and CocoIndex availability. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:121:| REQ-001 | `memory_context` must be described as additive query-intent enrichment, not exclusive backend routing. | **Given** a structural or hybrid query, **when** `memory_context` handles it, **then** the docs state that normal semantic strategy execution still runs and optional `graphContext` is appended when available rather than replacing the main path. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:122:| REQ-002 | The response metadata contract must be documented as `queryIntentRouting`. | **Given** a documented `memory_context` response, **when** the metadata object is described, **then** it is named `queryIntentRouting` and lists `queryIntent`, `routedBackend`, `confidence`, and optional `matchedKeywords`, with no `fallbackApplied` field. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:123:| REQ-003 | `session_resume` must match the current schema and output behavior. | **Given** `session_resume`, **when** its behavior is documented, **then** the docs say it accepts only `specFolder?` and `minimal?`, calls `memory_context({ mode: "resume", profile: "resume" })` unless `minimal` is true, returns `codeGraph { status, lastScan, nodeCount, edgeCount, fileCount }`, and returns `cocoIndex { available, binaryPath }` without calling `ccc_status()`. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:138:- **SC-001**: The packet consistently describes `memory_context` as semantic-first execution with optional graph enrichment for structural or hybrid queries.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:140:- **SC-003**: Every file that mentions `session_resume` describes the slim graph and CocoIndex summaries and omits `ccc_status()` claims.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:152:| Risk | Overstating `routedBackend` semantics as hard dispatch | High | Explicitly describe it as metadata on an additive enrichment flow, not as a guarantee that the request left `memory_context`. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:181:- No graph context built: `memory_context` still returns the traced semantic result without routing away from its normal path.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:185:- CocoIndex unavailable: `session_resume` exposes `cocoIndex.available = false` with a fixed `binaryPath`, not a full status dump.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:191:- Resume after idle session: `session_resume` combines resume context with lightweight graph and CocoIndex summaries.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/spec.md:201:| Scope | 18/25 | Cross-tool contract alignment across `memory_context`, `session_resume`, and passive enrichment. |
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:2:title: "Phase 010: CocoIndex Bridge + Context [system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec]"
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:3:description: "Implement code_graph_context, the LLM-oriented orchestration tool that bridges CocoIndex semantic search results into structural graph neighborhoods. Accepts native CocoIndex MC..."
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:23:# Phase 010: CocoIndex Bridge + code_graph_context
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:78:Implement `code_graph_context`, the LLM-oriented orchestration tool that bridges CocoIndex semantic search results into structural graph neighborhoods. Accepts native CocoIndex MCP result objects as seeds, resolves them to graph nodes, expands structurally, and returns compact context packages optimized for AI consumption.
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:82:- CocoIndex Code MCP returns: `file`, `lines`, `snippet`, `score`, `language` per hit
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:91:- **Native seed acceptance**: CocoIndex MCP results accepted directly — no intermediate conversion required by callers
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:99:interface CocoIndexSeed {
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:212:Seed: src/auth/middleware.ts:10-42 (CocoIndex score 0.91)
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:248:- Optional: reverse semantic augmentation (graph neighbors → scoped CocoIndex query)
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:268:- [ ] `code_graph_context` accepts native CocoIndex MCP result objects in `seeds[]`
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/spec.md:269:- [ ] All seed types (CocoIndex, Manual, Graph) normalize to `ArtifactRef`
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:95:- `memory_context({ mode: "resume" })` — resume-tuned retrieval with 1200-token budget
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:98:- Constitutional memories auto-surface on every `memory_context` call
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:100:**Key gap found (iteration 012):** `memory_context({ mode: "resume" })` returns search-style results, NOT a compact brief. Must also pass `profile: "resume"` for the brief `{ state, nextSteps, blockers }` format. Current `/spec_kit:resume` command does NOT pass `profile: "resume"`.
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:116:  1. Output tool availability guidance (Spec Kit Memory tools, CocoIndex status, Code Graph tools)
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:122:  2. Output resume instructions (tells AI to call memory_context with resume profile)
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:134:This is intentional. Hooks run as CLI commands with stdout capture, so they cannot call MCP tools directly during injection. Instead, the hook prints concise instructions into the session context, and the AI reads those instructions and acts on them. For example, the resume path tells the AI to call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` itself.
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:157:1. **One retrieval contract across all runtimes** — hooks point the AI at the same `memory_context()` and `memory_match_triggers()` flows that manual work uses
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:159:3. **`/spec_kit:resume` remains canonical** — the hybrid design keeps that contract and directs the AI to use `memory_context({ mode: "resume", profile: "resume" })` when a resume brief is needed
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:174:| Tool availability | 700 | Spec Kit Memory tools, CocoIndex status, Code Graph tools |
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:175:| Resume instructions | 700 | Tell the AI which `memory_context(..., profile: "resume")` call to make |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-092.md:37:| 079 | Q16 CocoIndex/code-graph implementation claims | 1 | 1 | 5 | 0 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-092.md:67:4. The performance story from Segment 6 mixed measured constants with projected pipeline behavior. `HOOK_TIMEOUT_MS` is still `1800`, but the live timeout only wraps stdin parsing, and the richer graph/CocoIndex latency figures are not instrumented facts in the present hook path.[SOURCE: .opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:15-31][SOURCE: .opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:82-113]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-092.md:80:8. **Two externally visible issues surfaced outside the original Segment 6 scope:** the startup Working Memory branch is effectively unreachable because no in-repo producer writes `workingSet`, and both `memory_context` and `code_graph_context` still reflect raw internal exception text back to callers.[SOURCE: .opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-091.md:32-40][SOURCE: .opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-091.md:56-65]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-092.md:97:The nuance remains the same as the earlier D3 review: the hook *does* call `mergeCompactBrief()`, but the inputs are still not a real retrieval-backed Memory + Code Graph + CocoIndex merge. `constitutional` and `triggered` are still hardcoded to empty strings, `codeGraph` is built from transcript-derived active file paths, and `cocoIndex` is still only a literal advisory sentence telling the agent to run CocoIndex later. So the review finding stands: the docs overstate what the current hook path actually does.[SOURCE: .opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:141-203][SOURCE: .opencode/specs/system-spec-kit/024-compact-code-graph/review/iterations/iteration-004.md:7-11]
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:4:description: "Implementation order for query-intent enrichment in memory_context, session_resume, and passive enrichment."
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:69:This phase adds query-intent awareness without replacing `memory_context`'s core semantic flow. The shipped implementation classifies intent, optionally appends graph context for structural or hybrid queries, exposes `queryIntentRouting` metadata, adds a slim `session_resume` composite tool, and wires passive enrichment into the response path.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:83:- [x] `session_resume` is described without `ccc_status()` or full CocoIndex status claims.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:96:- **`handlers/session-resume.ts`**: Returns resume context, summarized code graph stats, and CocoIndex availability.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:101:User query enters `memory_context`, query intent is classified, the normal traced semantic result is produced, and graph context is appended only when structural or hybrid signals justify it and context can be built. `session_resume` separately combines memory resume data with graph and CocoIndex summaries rather than proxying full status-tool payloads.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:109:- Classify query intent near the top of `memory_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:117:- Return `memory_context` resume data, `codeGraph { status, lastScan, nodeCount, edgeCount, fileCount }`, and `cocoIndex { available, binaryPath }`.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:132:| Contract audit | `memory_context` metadata and enrichment behavior | Verified handler line references |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:145:| `graphDb.getStats()` + `isCocoIndexAvailable()` | Internal | Green | `session_resume` cannot expose its lightweight status summary. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:169:| Query Intent | Existing `memory_context` semantic flow | Resume metadata accuracy, final verification |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/plan.md:191:- [x] Existing `memory_context` behavior preserved as the semantic baseline.
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan.md:2:title: "Plan: Phase 010 — CocoIndex Bridge + [system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan]"
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan.md:23:# Plan: Phase 010 — CocoIndex Bridge + code_graph_context
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan.md:85:    - Optional reverse semantic augmentation: expanded graph neighbors → CocoIndex search
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan.md:92:4. **Test with real CocoIndex results:**
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan.md:93:    - Run CocoIndex search → feed results as seeds to code_graph_context
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan.md:108:- CocoIndex Code MCP (for semantic seeds — already deployed)
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/plan.md:117:| CocoIndex unavailable | Proceed without seeds, use subject or outline fallback |
.opencode/specs/system-spec-kit/024-compact-code-graph/027-opencode-structural-priming/spec.md:99:- CocoIndex semantic-search improvements unrelated to first-turn structural bootstrap
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:9:| `@context-prime` agent | `memory_context(resume)` -> `code_graph_status` -> `ccc_status` -> `session_health` | Heavy, because the first call dominates | Best manual "full recovery" experience |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:11:| `session_resume` | `handleMemoryContext(resume)` + graph stats + CocoIndex availability | Medium-heavy; still dominated by resume retrieval | Single-call recovery without `session_health` |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:15:- `memory_context(resume)` routes to `executeResumeStrategy()`, which calls `handleMemorySearch()` with `limit=5`, `includeContent=true`, anchors `['state','next-steps','summary','blockers']`, `enableDedup=false`, `useDecay=false`. This is the expensive part because it performs real retrieval and ranking work.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:16:- `primeSessionIfNeeded()` does not call `memory_context`; it uses a cached constitutional-memory query, a code-graph snapshot, and a cheap package builder.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:26:| `memory_context(resume)` | DB readiness check, resume-mode orchestration, `memory_search`, ranking, content inclusion, anchors | **Very high** | Only path doing full retrieval/search/scoring |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:28:| `ccc_status` / `isCocoIndexAvailable()` | `existsSync` plus optional stat checks | **Very low** | Filesystem existence check |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:35:Cold-start cost is overwhelmingly concentrated in `memory_context(resume)`. The other three `@context-prime` calls are not the problem:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:47:| `memory_context(resume)` | **High for resume**, low for fresh-task starts | Needed only when recovering prior work |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:49:| CocoIndex availability | **Medium** | Helpful, but not strictly required for a productive first turn |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:74:- CocoIndex availability is useful but not essential.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:98:- CocoIndex availability
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:122:- `session_resume` already bundles the only expensive thing that matters (`memory_context(resume)`) plus graph + CocoIndex.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:147:- optional CocoIndex bit
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:154:- optionally omit CocoIndex if strict minimum is desired
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:175:- `isCocoIndexAvailable()`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:180:This tool would **not** call `memory_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-108.md:262:- CocoIndex optional
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/plan.md:75:   - Optionally query CocoIndex for code context related to current spec folder
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/plan.md:76:   - `source=resume` → `memory_context({ mode: "resume", profile: "resume" })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:68:### 4. Claim: CocoIndex costs ~100-500ms and cannot be used in the hook path
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:71:The current PreCompact hook does **not** make a CocoIndex call. Instead, when active files are found, it places a **literal hint string** into the `cocoIndex` field:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:75:That string is then passed into `mergeCompactBrief()` as one of the merge inputs. In other words, the current hook path does not perform a live CocoIndex MCP roundtrip; it merely injects a post-recovery suggestion.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:77:This supports the practical conclusion that the current hook path cannot rely on live CocoIndex results. But the numeric `~100-500ms` roundtrip estimate is **not verifiable from current timing code**, because no such request is made here.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:91:- live CocoIndex search
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:133:- CocoIndex roundtrip (`~100-500ms`)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:137:The biggest correction is conceptual: **the current PreCompact hook is still a lightweight transcript-analysis + merge + cache-write path, not the fully enriched graph/CocoIndex pipeline described in iteration 070.**
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-082.md:142:- Treating the prior SQLite, CocoIndex, or tree-sitter latency numbers as currently instrumented facts
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:5:Determine how a query-intent router should distinguish structural code questions from semantic code questions, decide when to route first to CocoIndex, a future code graph, or memory, and define an MVP that fits the current Spec Kit Memory search pipeline without overloading the existing causal-memory `graph` channel.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:15:   The existing intent classifier's 7 categories (`add_feature`, `fix_bug`, `refactor`, `security_audit`, `understand`, `find_spec`, `find_decision`) are useful for weighting memory retrieval, but they are too coarse for deciding between CocoIndex and a future code graph. For code queries, the minimum useful intent set is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:28:   - CocoIndex answers resemblance and concept similarity
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:56:   | `structural_navigation` | Code Graph | CocoIndex | Memory | Graph-first, semantic expansion only if anchor weak |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:57:   | `semantic_discovery` | CocoIndex | Code Graph | Memory | Semantic-first, then graph-expand top anchors |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:58:   | `impact_analysis` | Code Graph | Memory | CocoIndex | Graph-first neighborhood + memory constraints |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:59:   | `execution_path` | Code Graph | CocoIndex | Memory | Graph-first if concrete anchor exists; otherwise semantic-first |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:60:   | `decision_context` | Memory | CocoIndex | Code Graph | Memory-first, graph only after code anchor identified |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:61:   | `mixed_code_lookup` | CocoIndex | Code Graph | Memory | Two-stage semantic-to-graph cascade |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:73:     Example: run CocoIndex first, extract 1-3 anchors, then run code graph on those anchors
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:104:   - Layer 2a: CocoIndex request
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:106:   - Layer 2c: memory request via existing `memory_context` / `memory_search`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:124:   2. run CocoIndex first to find likely candidate files/symbols
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:147:   - if the prior route was memory-first and the user pivots to implementation impact, carry forward the memory constraint but switch primary to graph or CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:178:   - `semantic_discovery` -> CocoIndex only
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:180:   - `decision_context` -> memory then CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-048.md:181:   - `mixed_code_lookup` -> CocoIndex then code graph
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-020.md:10:3. Session IDs are server-minted and server-trusted. If a caller omits `sessionId`, `resolveTrustedSession()` generates a UUID and treats it as the `effectiveSessionId`. If a caller supplies one, it must already be tracked and identity-bound, or the server rejects it. `memory_context` then passes only `effectiveSessionId` downstream and exposes it in response metadata. ([session-manager.ts:385](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts#L385), [session-manager.ts:396](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts#L396), [session-manager.ts:401](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts#L401), [memory-context.ts:1060](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts#L1060), [memory-context.ts:955](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts#L955))
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-020.md:18:7. The bridge rule for `hook-state.ts` should be: never pass Claude’s raw `session_id` into Spec Kit as `sessionId`. That value is not trusted unless the server already minted and tracks it. The hook should store a local mapping `claudeSessionId -> effectiveSessionId`, mint the Spec Kit ID via `memory_context` on first contact, and reuse only the returned `effectiveSessionId` afterward. `memory_match_triggers` already documents this contract in its recovery hint. This is an inference from the trust model, but it is strongly implied by the server’s validation path. ([session-manager.ts:401](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts#L401), [memory-context.ts:1049](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts#L1049), [memory-context.ts:1056](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts#L1056), [memory-triggers.ts:207](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts#L207), [memory-triggers.ts:225](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts#L225))
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-020.md:22:9. `hooks/index.ts` is only a barrel right now, so `hook-state.ts` should slot in as another exported hook utility rather than inventing a separate loading path. For recovery, the safest fallback is: if local hook state is missing or invalid, mint a new `effectiveSessionId`, then use semantic resume (`memory_context` in `resume` mode plus `specFolder`) to recover work context even if strict session continuity is gone. ([hooks/index.ts:4](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/index.ts#L4), [memory-context.ts:581](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts#L581), [memory-context.ts:691](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts#L691), [memory-context.ts:1228](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts#L1228))
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-020.md:42:- On first use, call `memory_context` without `sessionId`, read back `sessionLifecycle.effectiveSessionId`, and persist the mapping. Never send raw Claude `session_id` into MCP tools.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-020.md:43:- On reuse, pass only the cached `effectiveSessionId`. If the server returns session-scope rejection, delete the mapping, mint a new session, and fall back to `memory_context({ mode: "resume", specFolder, ... })`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-071.md:29:   - **Level 0 (full)**: Code Graph + CocoIndex + Memory (3-source merge) -- current happy path
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-071.md:30:   - **Level 1 (graph-down)**: CocoIndex + Memory only. Trigger: `initDb()` throws or `getStats()` returns null. Action: skip codeGraph section in MergeInput, log warning, continue with 2-source merge
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-071.md:31:   - **Level 2 (graph+coco-down)**: Memory only. Trigger: CocoIndex binary missing (`checkCocoIndexAvailable()` returns not-installed) AND graph unavailable. Action: use constitutional + triggered memories only
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-071.md:32:   - **Level 3 (all-down)**: Bare session recovery. Trigger: MCP server itself unreachable. Action: instruction-file-based prompts (CLAUDE.md, CODEX.md) tell the AI to call `memory_context` on first interaction
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-071.md:33:   - Implementation: A `DegradationLevel` enum (0-3) computed once per session via a `computeDegradationLevel()` function that probes each source. The level is passed into `mergeCompactBrief` to adjust budget allocation (e.g., at Level 1, code graph's 1200-token floor reallocates to CocoIndex and memory).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:11:   The current packet already proves that our compaction path needs a concise, budgeted payload rather than raw search output: `context-server.ts` treats `memory_context(mode:"resume")` as a compaction lifecycle call, routes it through `autoSurfaceAtCompaction()`, and stores surfaced context in response metadata before budget enforcement. `autoSurfaceAtCompaction()` itself is already a bounded preservation hook with a dedicated 4,000-token budget. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:325-399`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:52-55`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:283-317`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:30:   Semantic retrieval is strong at "find code related to this concept." Structural retrieval is stronger at "what must I keep so the model can continue this exact implementation thread?" The packet's own search internals already separate these concerns: the current `graph` channel is a causal-memory graph over memories, not a code-structure graph, while CocoIndex is a chunk-embedding semantic channel. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/query-router.ts:23-72`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:1-220`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-033.md`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:50:     Conceptual similarity and natural-language relevance. "authentication retry flow", "context compaction", "resume brief", "how does startup recovery work?" This is where CocoIndex-style embeddings and memory semantic search shine.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:173:      `SessionStart(source=resume)`: use `memory_context({ mode: "resume", profile: "resume" })` and optionally augment with graph-derived working-set reconstruction.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:175:   This preserves the packet's existing decisions: hooks remain transport, `memory_context` remains the canonical resume primitive, and code graph stays a sibling retrieval channel rather than a replacement for semantic search. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md:72-77`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:16-36`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:48-74`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-033.md`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:204:     if graph data is missing or stale, degrade to current `memory_context(... profile:"resume")` + auto-surface behavior
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:207:     full cross-language graph completeness, learned ranking, UI graph inspection, graph-aware MCP query tools, incremental AST retention in memory, or replacing CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:246:Earlier iterations established the individual pieces: Claude lifecycle hooks, resume formatting, tree-sitter viability, aider repo-map, and CocoIndex separation. This iteration adds the missing synthesis layer. The new value is the architecture answer to "how does code graph concretely improve compaction?" rather than "is code graph interesting in general?" Specifically, it defines:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:262:7. Keep `memory_context({ mode: "resume", profile: "resume" })` as the canonical fallback when graph data is missing.
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/checklist.md:89:- [x] CocoIndex score-propagation limitation is documented accurately as deferred [EVIDENCE: Phase 016 tasks and implementation summary record the API dependency]
.opencode/specs/system-spec-kit/024-compact-code-graph/review/iterations/iteration-003.md:25:- P2-003: Public traceability surfaces for `session_resume` still describe the pre-ladder implementation. The feature catalog says the handler performs a `memory_context(mode=resume, profile=resume)` sub-call [SOURCE: .opencode/skills/system-spec-kit/feature_catalog/22--context-preservation-and-code-graph/18-session-resume-tool.md:14], and the manual playbook repeats that same validation target while also expecting `codeGraph.status in [ok, empty, error]` [SOURCE: .opencode/skills/system-spec-kit/manual_testing_playbook/22--context-preservation-and-code-graph/263-session-resume.md:17] [SOURCE: .opencode/skills/system-spec-kit/manual_testing_playbook/22--context-preservation-and-code-graph/263-session-resume.md:25]. The live handler now uses `buildResumeLadder()` for packet recovery and returns freshness states `fresh|stale|empty|error` [SOURCE: .opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:34] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:423] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:443]. That leaves operator docs and test prompts misaligned with the shipped recovery surface.
.opencode/specs/system-spec-kit/z_archive/013-memory-overhaul-and-agent-upgrade-release/003-command-alignment/changes.md:20:- Updated to align with current memory_context behavior
.opencode/specs/system-spec-kit/z_archive/013-memory-overhaul-and-agent-upgrade-release/003-command-alignment/changes.md:44:**Verification**: Manual accuracy check against `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts` for memory_context, memory_save, and memory_index_scan parameters
.opencode/specs/system-spec-kit/z_archive/013-memory-overhaul-and-agent-upgrade-release/003-command-alignment/changes.md:94:- Reordered session detection priority: run memory_match_triggers() before memory_context()
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-068.md:37:**Goal:** Make code graph and CocoIndex context flow automatically into AI conversations without explicit tool calls.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-068.md:63:| `mcp_server/handlers/memory-context.ts` | 1373 | Add priming payload assembly for code graph context | +30-40 | Include code_graph_context summary in first memory_context response |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-068.md:82:- B2: Start a new MCP session (no prior calls), call `memory_context`, verify response includes code graph summary.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-068.md:83:- B3: Call a tool that references a file (e.g., `memory_search` returning a file path), verify response envelope includes structural context for that file.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-068.md:254:- `seed-resolver.ts` (267 lines) -- CocoIndex integration seam
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/tasks.md:77:- [x] Item 42: CODEX.md updated with Session Start Protocol — Evidence: calls `memory_context()` with resume profile + `code_graph_status()` on first turn
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/tasks.md:90:- [x] CocoIndex score-propagation follow-up remains explicitly deferred because the required API support is still absent
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-014.md:36:- `context-server.ts` already treats `memory_context({ mode: "resume" })` as the compaction-aware memory path.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-014.md:38:- `memory_context` already has a dedicated `resume` strategy and supports `profile: "resume"`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-014.md:263:### Why not call `memory_context()` directly from the hook script?
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-014.md:387:memory_context({
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-014.md:855:- [SOURCE: .opencode/skills/system-spec-kit/mcp_server/context-server.ts] - current runtime wiring for `memory_context`, auto-surface, and compaction-aware dispatch
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/012-handover-triggers/scratch/legacy-memory-quarantine/17-12-25_16-19__handover-triggers.md:348:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "004-speckit/007-handover-triggers" })` |
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/012-handover-triggers/scratch/legacy-memory-quarantine/17-12-25_16-19__handover-triggers.md:353:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/implementation-summary.md:92:- **AGENTS.md**: Calls `memory_context()` with resume profile + `code_graph_status()` on first turn
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/implementation-summary.md:103:Five v1 checklist items that overstated shipped behavior now carry PARTIAL annotations with specific reasons: resume profile documentation gaps, tree-sitter vs regex indexer description, 3-source hook pipeline overclaiming, CocoIndex semantic neighbors not retrieved, and working-set-driven ranking not wired.
.opencode/specs/system-spec-kit/024-compact-code-graph/016-cross-runtime-ux/implementation-summary.md:154:2. **CocoIndex score propagation not implemented.** Near-exact confidence is based on line distance only. Blending with CocoIndex relevance scores requires API work.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-005.md:45:Our system mandates: Gate 1 triggers `memory_match_triggers()` first, then Gate 2 runs `skill_advisor.py`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-005.md:81:- Provide marginal benefit over our existing CocoIndex Code + Memory MCP (LOW value-add)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-078.md:12:- **T2 instruction-file triggers** is confirmed in a narrower form than some prior writeups implied. `CODEX.md` still instructs the agent to call `memory_context(... mode: "resume" ...)` after compaction and lists code graph tools in routing/tool sections, but it does **not** contain a "Session Start Protocol" or any automatic `code_graph_status()` / `code_graph_scan()` step.  
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-078.md:14:- **T4 Gate 1 automatic** is confirmed. The root `CLAUDE.md` still requires `memory_match_triggers(prompt)` on each new user message.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-078.md:59:Some agent bodies still reference CocoIndex/code graph tools in their instructions, so tool awareness exists in content. But explicit frontmatter MCP bindings are currently visible only on a subset of agents, not all 10.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-078.md:84:- OpenCode/Codex still expose code graph and CocoIndex tools.
.opencode/specs/system-spec-kit/z_archive/018-mcp-issues-after-update/scratch/legacy-memory-quarantine/18-02-26_09-47__mcp-issues-after-update.md:370:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/z_archive/018-mcp-issues-after-update" })` |
.opencode/specs/system-spec-kit/z_archive/018-mcp-issues-after-update/scratch/legacy-memory-quarantine/18-02-26_09-47__mcp-issues-after-update.md:382:memory_search({ specFolder: "system-spec-kit/z_archive/018-mcp-issues-after-update", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/018-mcp-issues-after-update/scratch/legacy-memory-quarantine/18-02-26_09-47__mcp-issues-after-update.md:388:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/018-mcp-issues-after-update/scratch/legacy-memory-quarantine/18-02-26_09-47__mcp-issues-after-update.md:397:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-029.md:7:1. The exact `/spec_kit:resume` -> `memory_context` invocation
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-029.md:18:1. `/spec_kit:resume` calls `memory_context` with the same four-field payload in both auto and confirm YAMLs: `input: "resume previous work continue session"`, `mode: "resume"`, `specFolder: "{...}"`, `includeContent: true`. The interactive workflow defines that payload once in `memory_loading.mcp_integration.parameters` and again in `workflow.step_3_load_memory.mcp_tool.parameters`; the autonomous workflow does the same in its `memory_loading` and `step_2_load_memory` blocks. The exact invocation is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-029.md:19:   `memory_context({ input: "resume previous work continue session", mode: "resume", specFolder: "{spec_folder_path|detected_spec_folder}", includeContent: true })`. [.opencode/commands/spec_kit/assets/spec_kit_resume_confirm.yaml:81-85] [.opencode/commands/spec_kit/assets/spec_kit_resume_confirm.yaml:182-186] [.opencode/commands/spec_kit/assets/spec_kit_resume_auto.yaml:78-82] [.opencode/commands/spec_kit/assets/spec_kit_resume_auto.yaml:138-142]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-029.md:21:2. `profile: "resume"` is missing from every executable `memory_context` parameter block in the resume workflow, even though the MCP contract explicitly supports `profile` for `memory_context` and enumerates `resume` as a valid value. In other words, the resume command is only selecting `mode: "resume"` today; it is not requesting the response formatter meant for resume-shaped output. The gaps are the four YAML parameter blocks above, while the schema and allowed-parameter lists already expose `profile`. [.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:40-44] [.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:100-116] [.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:453-455]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-029.md:43:memory_context({
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-029.md:109:1. The executable resume workflow is still missing `profile: "resume"` in all four `memory_context` parameter blocks even though the tool contract already supports it.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-029.md:115:1. Add `profile: "resume"` to all four `memory_context` invocations in:
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/checklist.md:2:title: "Checklist: Phase 010 — CocoIndex [system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/checklist]"
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/checklist.md:22:# Verification Checklist: Phase 010 — CocoIndex Bridge + code_graph_context
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/checklist.md:81:- [x] Accepts native CocoIndex MCP result objects in `seeds[]` (provider: 'cocoindex') — context handler maps provider-typed seeds [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/checklist.md:102:- [x] Reverse semantic augmentation: graph neighbors → scoped CocoIndex query — nextActions suggests CocoIndex [EVIDENCE: verified in implementation-summary.md]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:1:# Iteration 054: MCP Tool API - `code_graph_context` with CocoIndex Seeds
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:8:2. CocoIndex stays the semantic retrieval system of record.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:11:This iteration answers the remaining API-level questions: the full parameter schema, how `seeds` should accept CocoIndex results, what the LLM-facing output should look like, how budget enforcement should work, and whether the query-mode surface should explicitly distinguish `neighborhood`, `outline`, and `impact`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:62:2. `seeds[]` should accept raw CocoIndex MCP results directly, then normalize them internally to graph artifacts.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:64:   The CocoIndex MCP contract already returns exactly the fields the bridge needs: `file`, `lines`, `snippet`, `score`, and `language`. That means `code_graph_context` should not force the caller to convert those results into a different symbol-only object just to call the next tool. The bridge should accept a discriminated union that includes the native CocoIndex response shape.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:69:   type CodeGraphSeed = CocoIndexSeed | ManualSeed | GraphSeed;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:71:   interface CocoIndexSeed {
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:183:   Seed: src/auth/middleware.ts:10-42 (CocoIndex score 0.91)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:193:   - `semanticSeeds`: what CocoIndex found
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:270:  - explicitly states that `code_graph_context` should accept CocoIndex results as seeds for structural expansion
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:272:  - DR-010 locked the division of labor: CocoIndex for semantic retrieval, code graph for structural relationships
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:274:  - confirms CocoIndex MCP search returns `file`, `lines`, `snippet`, `score`, and `language`, which is the native seed shape the bridge should accept
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:291:- it closes the last bridge gap by letting `seeds[]` accept native CocoIndex MCP result objects directly
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:300:2. Accept native CocoIndex MCP search hits in `seeds[]` with `provider: 'cocoindex'`, `file`, `lines`, `snippet`, `score`, and `language`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:302:4. Keep `subject` for deterministic graph-native callers, but do not require it for CocoIndex-seeded flows.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-054.md:308:10. Treat this tool as the bridge surface only; keep exact graph operations in `code_graph_query` and keep semantic retrieval ownership in CocoIndex.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:49:| CocoIndex integration | **USE** — existing semantic layer, complements structural code graph | Iterations 036-045 + CocoIndex skill analysis |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:50:| CocoIndex ↔ Code Graph bridge | **BUILD** — file-range seeds, 1-hop expansion, reverse semantic augmentation | Iterations 046-055 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:51:| Token budget allocation | **FLOORS + OVERFLOW** — constitutional 700, graph 1200, CocoIndex 900, triggered 400, overflow 800 | Iteration 049 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:69:                       ├── memory_match_triggers(prompt)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:70:                       └── memory_context(mode:"resume", profile:"resume")
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:87:**memory_context Resume Flow** (Iteration 017):
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:88:- Resume brief lives in **inner** `memory_search` envelope, NOT outer `memory_context` envelope
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:92:  - memory_context layer: **2000** tokens
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:125:- Mint via `memory_context` on first contact, reuse `effectiveSessionId` thereafter
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:383:│  │ Memory  │  │  Code    │  │ CocoIndex │  │
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:391:│       memory_context + code_graph_context    │
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:392:│       + cocoindex_code search                │
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:410:│  │ CocoIndex (.cocoindex_code/)         │   │
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:423:6. **Phase 010**: code_graph_context + CocoIndex bridge — seed normalization, reverse semantic augmentation (3-4 days)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:438:| 5 | 046-055 | CocoIndex + Code Graph integration | 0.49-0.76 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:457:| 017 | 166 | memory_context resume flow |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:473:| 033 | 48 | CocoIndex integration options |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:486:| 046 | 284 | CocoIndex ↔ Code Graph bridge design |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:487:| 047 | 70 | tree-sitter ↔ CocoIndex chunk alignment |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:494:| 054 | 549 | code_graph_context API with CocoIndex seeds |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:499:## Part VI: CocoIndex Integration Impact
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:501:### What CocoIndex Already Covers
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:503:CocoIndex Code is deployed as an MCP server providing semantic code search via vector embeddings:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:514:| Build semantic index for code recall | **DROP** | CocoIndex already provides this |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:515:| Choose code embedding model | **DROP** | CocoIndex uses voyage-code-3 / all-MiniLM-L6-v2 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:516:| Implement code chunking for embeddings | **DROP** | CocoIndex handles function-level chunking |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:517:| Dual-index retrieval (code + text) | **DROP** | Already exists: CocoIndex (code) + Memory DB (text) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:518:| tree-sitter + SQLite structural graph | **KEEP** | Structural relationships CocoIndex can't provide |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:520:| Incremental graph updates (chokidar + git) | **KEEP** | Graph-specific, independent of CocoIndex |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:524:| Code graph API accepts CocoIndex results as seeds | **MODIFY** | Structural expansion of semantic hits |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:525:| Reranking uses graph edges for CocoIndex results | **MODIFY** | Structurally connected results rank higher |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:526:| Query-intent routing for code tasks | **MODIFY** | Route structural → code_graph, semantic → CocoIndex |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:527:| CocoIndex ↔ Code Graph bridge | **ADD** | Bidirectional enrichment between systems |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:533:| "Find code related to X" | CocoIndex (semantic) | Code graph (expand neighbors) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:536:| "How does retry logic work?" | CocoIndex (semantic) | Code graph (trace call chain) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:543:PreCompact pipeline (enriched with CocoIndex):
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:545:  2. CocoIndex: semantic neighbors of active symbols  ← EXISTING MCP
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:556:CocoIndex covering semantic search means the code graph can be **purely structural** and much simpler. No embeddings, no chunking, no vector search in the code graph at all. It becomes a lightweight relationship index that answers "what connects to what" while CocoIndex answers "what resembles what." The two complement each other without overlap.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:560:**Bridge Design** (iter 046): `code_graph_context` accepts file-range seeds directly from CocoIndex. Execution is parallel-then-sequential: Stage A (parallel semantic + graph bootstrap) → Stage B (cross-expansion) → Stage C (late fusion). Latency budget: <2s for PreCompact.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:562:**Chunk Alignment** (iter 047): CocoIndex uses structure-aware character chunking (~1000 chars), not true AST function-level splitting. Seed-to-node resolution: exact symbol → enclosing symbol → file anchor.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:564:**Intent Router** (iter 048): New top-level router separate from existing `query-router.ts`. Routes structural→code_graph, semantic→CocoIndex, session→Memory. MVP: keyword heuristics with telemetry.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:566:**Token Budget** (iter 049): Floors + overflow pool model. Constitutional 700, Graph 1200, CocoIndex 900, Triggered 400, Overflow 800. When a source is empty, its floor redistributes to overflow. Priority: constitutional > graph > CocoIndex > triggered.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:568:**Repo Maps** (iter 050): Query-ranked dynamic maps using typed graph edges + CocoIndex relevance scores. Improves on aider's flat reference counting.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:570:**Index Coordination** (iter 051): Independent refresh cycles for CocoIndex and Code Graph. Freshness state exposed in API. No shared event bus needed for v1.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:572:**Merge Strategy** (iter 052): Constitutional → graph → CocoIndex → triggered. Structured output sections. File-level deduplication.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:576:**API Design** (iter 054): Three query modes — neighborhood (expand around seeds), outline (structural overview), impact (reverse dependency). Seed types: CocoIndexSeed, ManualSeed, GraphSeed. Normalized to ArtifactRef internally.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:590:| Budget Allocator | Needs adaptive weighting by query intent (structural→more graph, semantic→more CocoIndex), usage-based learning, dynamic overflow proportional to context budget, source-quality scoring | P2 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:592:| Hook System | Needs incremental graph refresh on Stop hook, pre-compaction graph snapshot, hook-based CocoIndex re-index trigger, cross-runtime parity patterns | P1 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:608:**Automatic AI Utilization** (iter 057): Three-tier auto-enrichment architecture for code graph + CocoIndex without explicit tool calls:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:612:| T1: Session lifecycle | SessionStart / Compaction | Background incremental code_graph_scan + ccc_reindex; preload working set neighborhoods | Zero (background) | 300-500 tokens graph, 200-400 CocoIndex |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:614:| T3: Query-aware | memory_context/memory_search runs | Graph neighborhood expansion alongside semantic results; intent-based routing | Shares main budget | Via 3-source allocator (floors + overflow) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:620:- **Lazy per-file staleness checks via `ensureFreshFiles()`** (iter 067): On `code_graph_query`/`code_graph_context` call, extract touched file paths from results, run two-tier staleness check: (1) mtime fast-path comparing `statSync().mtimeMs` against stored `code_files.file_mtime_ms` (~1ms/file), (2) content hash verification only when mtime differs (~5-20ms/file). Hybrid sync/async reindex: <=2 stale files reindexed synchronously, 3-10 files deferred to async with `freshness.reindexInProgress: true` flag, >10 files triggers nextAction suggesting full scan. Requires `ALTER TABLE code_files ADD COLUMN file_mtime_ms INTEGER` schema extension (mirrors memory system's `memory_index.file_mtime_ms` pattern). CocoIndex coordination: code graph stores `lastStaleDetectedAt` timestamp; `ccc_status` checks it and triggers `ccc_reindex({ full: false })` if recent. Session-start batch: first MCP call triggers parallel `handleCodeGraphScan({ incremental: true })` + `cccReindex({ full: false })` via `resolveTrustedSession` session detection.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:641:| T2: Instruction-file triggers | CODEX.md / CLAUDE.md force memory_context() at session start | Codex CLI, Copilot, Gemini | Good (AI compliance dependent) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:643:| T4: Gate 1 automatic | CLAUDE.md Gate 1 forces memory_match_triggers() each message | All runtimes | Basic (triggered context only) |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:646:- **CODEX.md already implements T2**: Explicit compaction recovery instructions with `memory_context({ mode: "resume" })` as first action.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:657:- **Per-tool priming behavior**: memory tools get full recovery hints (interrupted sessions, last spec folder, graph freshness); code graph tools get index freshness warnings; CocoIndex tools get availability status.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:659:- **CODEX.md gap identified**: No instruction-level trigger for code_graph_status() on session start. Enhancement: add `code_graph_status()` to "Context Retrieval Primitives" as third cross-runtime primitive alongside memory_match_triggers and memory_context.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:676:**CocoIndex Utilization Improvements** (iter 059): Five improvement areas for better CocoIndex integration:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:681:   - Propagate CocoIndex similarity score into ArtifactRef confidence (currently discarded)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:689:   - Keyword pre-classification: "who calls X" -> Code Graph impact; "find code that does X" -> CocoIndex search
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:690:   - Confidence-based fallback: low CocoIndex similarity (<0.3) -> fall back to code graph; file_anchor resolution -> suggest CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:694:   - Structural expansion of semantic results: CocoIndex -> resolve seeds -> expand neighborhood automatically
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:695:   - Semantic enrichment of structural results: Code graph call chain -> CocoIndex finds similar non-connected code
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:696:   - Working set warm-up: code graph hot files + CocoIndex adjacent code on session start
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:698:5. **Underutilized CocoIndex features**:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:699:   - Language/path filters not passed through from code graph metadata to CocoIndex searches
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:715:- **Seed resolution** deepened: CocoIndex scores are discarded at integration seam, needs near-exact tier
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:749:| CocoIndex availability graceful degradation | Low | Partial |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:757:5. CocoIndex/Code Graph independence: true at index level, tightly integrated at query level
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:828:| 0 | Full | Code Graph + CocoIndex + Memory | Default | 3-source merge |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:829:| 1 | Graph-down | CocoIndex + Memory | `initDb()` throws or `getStats()` null | Skip codeGraph in MergeInput, log warning |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:830:| 2 | Graph+Coco-down | Memory only | CocoIndex binary missing AND graph unavailable | Constitutional + triggered memories only |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:833:Implementation: A `DegradationLevel` enum (0-3) computed once per session via `computeDegradationLevel()` that probes each source. Passed into `mergeCompactBrief` to reallocate token budgets (e.g., Level 1 moves code graph's 1200-token floor to CocoIndex and memory). Estimated: ~60 LOC.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:867:4. **USE** CocoIndex as complementary semantic layer -- no overlap with structural code graph
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:895:**Q16 -- CocoIndex Utilization** (iterations 059, 063):
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:897:- CocoIndex score propagation: similarity scores currently discarded at integration seam; blend into ArtifactRef confidence
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:930:| CocoIndex MCP roundtrip | N/A (not in hook path) | 100-500ms | Must be tool-dispatch-time only |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:939:- Level 0 (full): Code Graph + CocoIndex + Memory
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:940:- Level 1 (graph-down): CocoIndex + Memory (code graph DB unavailable)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1036:| **Codex CLI** | `AGENTS.md`, `.codex/agents/context.toml` | No native hooks | Force first-turn `memory_context(...)` + `code_graph_status()` via instructions; do not rely on hook-style implicit warmup | **~85%** |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1077:| 099 | Query-intent routing integration | Auto-routing in memory_context (A) + classification metadata (D) | 150-300 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1097:4. **session_resume composite tool** (Iter 101): Single MCP tool combining `memory_context(resume)` + `code_graph_status` + `ccc_status`. Saves 400-900 tokens and 2-4 request/response cycles per resume flow.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1099:5. **Query-intent routing in memory_context** (Iter 099): Wire orphaned `classifyQueryIntent()` into `memory_context` so structural queries auto-route to code graph. Universal benefit across all runtimes.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1129:3. **`classifyQueryIntent()` is ready to wire in.** The orphaned classifier returns `structural | semantic | hybrid` with confidence scores. Wiring it into `memory_context` as a backend router (not just a mode selector) would unify the query experience.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1146:| 017 | 166 | memory_context resume flow |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1162:| 033 | 48 | CocoIndex integration options |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1175:| 046 | 284 | CocoIndex-Code Graph bridge design |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1176:| 047 | 70 | tree-sitter-CocoIndex chunk alignment |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1183:| 054 | 549 | code_graph_context API with CocoIndex seeds |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1188:| 059 | ~200 | CocoIndex utilization: seed resolution, auto-reindex, hybrid queries |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:1199:| 070 | ~250 | Performance analysis: 1800ms budget, SQLite <10ms, CocoIndex 100-500ms |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:4:description: "Query-intent enrichment in memory_context, slim session_resume output, and passive enrichment wired into the response path."
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:70:You can ask code questions through `memory_context` without switching tools yourself, but the implementation does not hand the request off to a different primary backend. The handler now classifies query intent, keeps its normal semantic execution path, and appends graph-aware context when the query looks structural or hybrid and graph context can be built. The same phase also added a slim `session_resume` tool and wired passive enrichment into the response path.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:72:### `memory_context` Query-Intent Enrichment
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:74:`classifyQueryIntent()` is wired into `handlers/memory-context.ts` before the traced response is returned. For structural and hybrid queries, the handler may build graph context with `buildContext()` and append that result to the normal traced output. The existing semantic strategy execution still runs through `executeStrategy()`, so this is additive enrichment rather than selective routing away from `memory_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:81:1. calls `memory_context({ mode: "resume", profile: "resume" })` unless `minimal` is true
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:83:3. checks CocoIndex availability with `isCocoIndexAvailable()` and returns `cocoIndex { available, binaryPath }`
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:96:| `handlers/session-resume.ts` | Created | Added the composite resume tool with slim resume, graph, and CocoIndex summaries. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:109:The delivery happened in three layers. First, `memory_context` gained query-intent classification plus optional graph-context enrichment. Next, `session_resume` was added as a composite resume helper with a deliberately narrow schema and payload. Finally, passive enrichment was wired into `context-server.ts`, with the code graph symbol logic consolidated into `lib/enrichment/passive-enrichment.ts` instead of a separate helper file.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:118:| Keep `memory_context` semantic-first and append graph context opportunistically | This preserves existing behavior while still surfacing structural context when the classifier and graph builder can support it. |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:139:2. **Graph enrichment is conditional.** Structural or hybrid intent can append `graphContext`, but `memory_context` still succeeds without it.
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/implementation-summary.md:140:3. **`session_resume` is intentionally narrow.** It exposes lightweight graph and CocoIndex summaries only; consumers that need deeper diagnostics still need dedicated status tools.
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/tasks.md:2:title: "Tasks: CocoIndex Bridge + code_graph_context [system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/tasks]"
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/tasks.md:3:description: "Task tracking for code_graph_context orchestration tool bridging CocoIndex semantic search into structural graph neighborhoods."
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/tasks.md:24:# Tasks: Phase 010 — CocoIndex Bridge + code_graph_context
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/tasks.md:69:- [x] Implement `seed-resolver.ts` — `lib/code-graph/seed-resolver.ts`; accepts CodeGraphSeed[] from any provider (CocoIndex, Manual, Graph)
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/description.json:3:  "description": "Phase 010: CocoIndex Bridge + code_graph_context",
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:4:description: "Implemented code_graph_context orchestration tool bridging CocoIndex semantic search into structural graph neighborhoods with seed resolution, three query modes, and budget-aware formatting. 22/22 checklist items verified."
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:70:Phase 010 delivers the LLM-oriented orchestration layer that bridges CocoIndex semantic search results into structural graph neighborhoods. The `code_graph_context` tool accepts seeds from any provider (CocoIndex MCP, manual, graph), resolves them to graph nodes, expands structurally via Phase 009 queries, and returns compact context packages optimized for AI consumption.
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:74:The seed resolver normalizes three seed types (CocoIndex, Manual, Graph) into a unified `ArtifactRef` representation. CocoIndex seeds use `file` plus `range.start/end`, manual seeds resolve by `symbolName`, and graph seeds resolve by `symbolId`. Each seed follows a resolution chain: exact symbol overlap, near-exact symbol match within ±5 start lines, enclosing symbol, or raw file anchor. Every resolution carries a confidence score reflecting match quality. Overlapping seeds that resolve to the same graph node are deduplicated before expansion.
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:111:Implemented in plan order: seed-resolver first (foundation), then the context orchestrator with all three query modes, then server integration. Each query mode was tested with real CocoIndex results and manual seeds against indexed repository files to verify resolution chain correctness, expansion behavior, and budget compliance.
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:121:| Latency guard at 400ms | Reverse semantic augmentation involves a CocoIndex round-trip. 400ms leaves enough budget for response formatting without risk of tool timeout. |
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:133:| CocoIndex seeds accepted and resolved | Verified |
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/implementation-summary.md:149:1. **No live CocoIndex round-trip for reverse augmentation.** The `nextActions` suggests CocoIndex queries but does not execute them inline. Full bidirectional semantic-structural fusion is deferred.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/synthesis-106-110.md:24:The overlap is partial: both check graph status and CocoIndex, but only agent priming does memory resume and only MCP priming does constitutional memory injection and session-primed state management.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/synthesis-106-110.md:30:Cold-start latency is dominated by `memory_context(resume)` -- the other 3 calls in the bootstrap are nearly free. The existing `primeSessionIfNeeded()` already provides a sub-50ms minimum viable prime with graph freshness, CocoIndex availability, and recommended next calls.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/synthesis-106-110.md:60:6. Strengthen tool descriptions for `memory_context`, `session_resume`, `session_health` with recovery affordances
.opencode/specs/system-spec-kit/024-compact-code-graph/research/synthesis-106-110.md:63:7. Create `session_bootstrap()` composite tool that returns memory + graph + CocoIndex + health in one call
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/checklist.md:83:- [x] CHK-010 [P0] Packet no longer claims selective backend routing out of `memory_context` [Evidence: `spec.md` REQ-001; `implementation-summary.md` query-intent section]
.opencode/specs/system-spec-kit/024-compact-code-graph/010-cocoindex-bridge-context/graph-metadata.json:156:        "name": "real CocoIndex",
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/tasks.md:72:- [x] Implement `source=resume` path with `memory_context({ mode: "resume", profile: "resume" })` — Evidence: resume path surfaces prior work and last spec folder (checklist P1), profile: resume passed for compact brief format (checklist P0)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-060.md:207:The `PRIORITY_ORDER` is hardcoded as `['constitutional', 'codeGraph', 'cocoIndex', 'triggered']`. This means code graph always gets overflow before CocoIndex, regardless of whether the query is structural (prefers code graph) or semantic (prefers CocoIndex).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-060.md:275:The `createDefaultSources()` function hardcodes exactly 4 sources. Future sources (e.g., `memory_search` results, file system context) would require code changes.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-060.md:337:Consolidation iteration: Synthesize all Q13-Q16 findings into a coherent feature improvement roadmap with prioritized phases. The four questions are now fully answered — a consolidation pass would create an actionable implementation plan ordering the fixes by impact (endLine bug first, then missing edges, then tree-sitter migration, then budget allocator improvements, then auto-utilization, then non-hook UX, then CocoIndex improvements).
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/079-speckit-cognitive-memory/changes-manifest.md:318:| 4 | Main Handler | Modified | `memory_search()` - Call `apply_testing_effect()` after search completes |
.opencode/specs/system-spec-kit/024-compact-code-graph/020-query-routing-integration/tasks.md:70:- [x] T001 Audit `memory_context` implementation facts (`handlers/memory-context.ts`)
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/implementation-summary.md:81:- **`source=startup`**: Outputs tool availability guidance listing Spec Kit Memory tools, CocoIndex status, and Code Graph tools. Checks for stale code graph index (>24h) and warns if needed. Does not perform active retrieval.
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/implementation-summary.md:82:- **`source=resume`**: Outputs resume instructions directing the AI to call `memory_context` with resume profile. Shows `lastSpecFolder` from hook state if available. Does not call `memory_context` directly.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-093.md:52:4. Sanitize externally returned exception strings from `memory_context` and `code_graph_context`.
.opencode/specs/system-spec-kit/024-compact-code-graph/review/deep-review-strategy.md:42:- CocoIndex semantic discovery may be unavailable in this environment, so direct file reads and exact search may be required.
.opencode/specs/system-spec-kit/024-compact-code-graph/review/deep-review-strategy.md:92:- Feature-catalog/playbook mirrors for `session_resume` still describe the older `memory_context` sub-call model and stale graph-status expectations.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:15:{"type":"iteration","run":13,"status":"complete","focus":"Hybrid hook+tool architecture design","findingsCount":6,"newInfoRatio":0.44,"noveltyJustification":"First design connecting Claude hooks, Gate 1, memory_context resume, and MCP auto-surface","timestamp":"2026-03-29T09:44:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:22:{"type":"iteration","run":17,"status":"insight","focus":"memory_context resume flow — nested envelope, 3 budget layers","findingsCount":9,"newInfoRatio":0.84,"noveltyJustification":"Resume brief lives in inner envelope, ResumeProfile includes topResult, 3 distinct token budgets (1200/2000/4000)","timestamp":"2026-03-30T10:20:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:37:{"type":"iteration","run":33,"status":"complete","focus":"CocoIndex Code integration options","findingsCount":7,"newInfoRatio":0.65,"noveltyJustification":"Semantic search vs structural graph, separate concerns, possible shared embedding","timestamp":"2026-03-30T10:37:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:52:{"type":"event","event":"segment_start","segment":5,"focus":"CocoIndex + Code Graph Integration Research","method":"GPT-5.4 codex agents, high reasoning, 2 waves of 5 parallel","timestamp":"2026-03-30T16:30:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:53:{"type":"iteration","run":46,"status":"complete","focus":"CocoIndex ↔ Code Graph Bridge Design","findingsCount":10,"newInfoRatio":0.75,"noveltyJustification":"Bridge API contract, seed shape, expansion behavior, reverse enrichment, latency budget","timestamp":"2026-03-30T17:00:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:54:{"type":"iteration","run":47,"status":"complete","focus":"tree-sitter ↔ CocoIndex Chunk Alignment","findingsCount":8,"newInfoRatio":0.68,"noveltyJustification":"Chunk boundary mapping, structure-aware chunking vs function-level, source map design","timestamp":"2026-03-30T17:00:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:56:{"type":"iteration","run":50,"status":"complete","focus":"Compact Repo Map Generation — Structural Graph + CocoIndex","findingsCount":10,"newInfoRatio":0.76,"noveltyJustification":"Aider repo-map analysis, typed graph improvement, CocoIndex ranking influence, MVP map design","timestamp":"2026-03-30T17:00:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:57:{"type":"iteration","run":51,"status":"complete","focus":"Incremental Index Coordination — CocoIndex + Code Graph Sync","findingsCount":10,"newInfoRatio":0.65,"noveltyJustification":"Independent refresh cycles, freshness metadata, branch switch handling","timestamp":"2026-03-30T17:00:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:60:{"type":"iteration","run":49,"status":"complete","focus":"Token Budget Allocation Across 3 Context Sources","findingsCount":10,"newInfoRatio":0.71,"noveltyJustification":"Three-source allocator with floors+overflow, priority order, CocoIndex token estimation, SessionStart budget profile","timestamp":"2026-03-30T18:15:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:61:{"type":"iteration","run":55,"status":"complete","focus":"Implementation Readiness — CocoIndex-Aware Code Graph Architecture","findingsCount":10,"newInfoRatio":0.65,"noveltyJustification":"Final synthesis: phase 008+ specs, readiness scorecard, MVP scope, LOC estimates","timestamp":"2026-03-30T18:15:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:62:{"type":"iteration","run":54,"status":"complete","focus":"MCP Tool API — code_graph_context with CocoIndex Seeds","findingsCount":10,"newInfoRatio":0.74,"noveltyJustification":"Full parameter schema, seed normalization, output format, budget enforcement, query modes","timestamp":"2026-03-30T18:30:00.000Z"}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:68:{"type":"iteration","run":59,"status":"complete","focus":"CocoIndex utilization improvements — seed resolution, auto-reindexing, query routing, hybrid patterns","findingsCount":5,"newInfoRatio":0.80,"noveltyJustification":"4 of 5 findings are fully new (near-exact seed resolution, auto-reindex triggers, hybrid query patterns, underutilized features); intent router improvement partially builds on segment 5 research","keyQuestions":["Q16"],"answeredQuestions":["Q16"],"ruledOut":["real-time file watcher for CocoIndex","LSP integration for query routing"],"focusTrack":"cocoindex-utilization","timestamp":"2026-03-31T14:45:00.000Z","durationMs":480000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:70:{"type":"iteration","run":63,"status":"complete","focus":"Q16 DEEP DIVE — seed resolution chain, auto-reindex, hybrid queries, CocoIndex MCP tools","findingsCount":8,"newInfoRatio":0.75,"noveltyJustification":"6 of 8 findings are new implementation-level designs (near-exact tier with confidence formula, score propagation blend, stale-triggered auto-reindex, hybrid query patterns A/B/C, missing composite index); 2 deepen prior findings (CocoIndex 1-tool limitation, computeFreshness coarseness)","keyQuestions":["Q16"],"answeredQuestions":["Q16"],"ruledOut":["SQLite editdist3 for fuzzy names","real-time file watcher","extending CocoIndex native MCP"],"focusTrack":"cocoindex-utilization","timestamp":"2026-03-31T15:30:00.000Z","durationMs":420000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:75:{"type":"iteration","run":67,"status":"complete","focus":"Auto-indexing and staleness detection design — stale-on-read mechanism with per-file granularity","findingsCount":8,"newInfoRatio":0.72,"noveltyJustification":"6 of 8 findings new (mtime fast-path gap, per-file staleness vs global MAX, ensureFreshFiles function design, hybrid sync/async threshold, schema extension with file_mtime_ms, CocoIndex freshness coordination); 2 deepen prior findings (content hash mechanism details from iter-063, computeFreshness coarseness from iter-063)","keyQuestions":[],"answeredQuestions":["Auto-indexing mechanism design","Staleness detection with latency constraints","CocoIndex coordination"],"ruledOut":["file watchers","global-only freshness check","synchronous reindex for all stale files"],"focusTrack":"auto-indexing","timestamp":"2026-03-31T18:00:00.000Z","durationMs":420000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:78:{"type":"iteration","run":70,"status":"complete","focus":"PERFORMANCE AND LATENCY ANALYSIS — hook timeout budget, SQLite query costs, token estimation accuracy, CocoIndex latency, pipeline latency budget design","findingsCount":8,"newInfoRatio":0.72,"noveltyJustification":"6 of 8 findings are new (1700ms headroom quantification, SQLite 1-9ms 1-hop expansion, token estimation 15-25% error margin, CocoIndex 100-500ms MCP roundtrip, tree-sitter 5-50ms per file, full pipeline latency budget table); 2 partially new (staleness check cost deepens iter-067 design, expandAnchor 400ms deadline budget confirms iter-061)","keyQuestions":[],"answeredQuestions":["Hook budget headroom","SQLite query costs","Token estimation accuracy","CocoIndex latency","Pipeline latency budget"],"ruledOut":["CocoIndex in hook path","synchronous tree-sitter reindex >3 files in hook"],"focusTrack":"performance-analysis","timestamp":"2026-03-31T20:30:00.000Z","durationMs":420000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:87:{"type":"iteration","run":79,"status":"complete","focus":"VERIFY Q16 findings from iterations 059 and 063 against current code in seed-resolver.ts, code-graph-db.ts, code-graph-context.ts, and CocoIndex MCP registration","findingsCount":7,"newInfoRatio":0.74,"noveltyJustification":"5 of 7 prior Q16 claims were disproven as current implementation, 1 was confirmed (native CocoIndex MCP exposes only search, with management surfaced through wrappers), and 1 was narrowed to a partial confirmation (missing composite index exists but performance necessity is not proven by live code).","keyQuestions":["Which Q16 findings from iterations 059 and 063 are actually implemented in current code?"],"answeredQuestions":["Which Q16 findings from iterations 059 and 063 are actually implemented in current code?"],"ruledOut":["Treating Q16 design proposals as shipped behavior","Inferring auto-reindex from freshness/staleness helpers alone","Inferring hybrid query execution from CocoIndex seed support alone"],"focusTrack":"verification","timestamp":"2026-03-31T13:44:00.000Z","durationMs":780000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:90:{"type": "iteration", "run": 77, "status": "complete", "focus": "VERIFY Q14 findings from iterations 057 and 061 against current code: auto-enrichment tiers, GRAPH_AWARE_TOOLS, pre-dispatch interception, MEMORY_AWARE_TOOLS double-check, and latency-budget implications", "findingsCount": 5, "newInfoRatio": 0.38, "noveltyJustification": "Primarily a verification pass. Two Q14 claims remain directly supported by current code (pre-dispatch interception and MEMORY_AWARE_TOOLS double-check). Three claims were narrowed from implementation-sounding statements to design-only proposals (three-tier graph/CocoIndex auto-enrichment, GRAPH_AWARE_TOOLS, and Promise.allSettled orchestration).", "keyQuestions": ["Do the five Q14 claims from iterations 057 and 061 still match the current implementation?"], "answeredQuestions": ["Three-tier graph/CocoIndex auto-enrichment is not implemented in the current code", "GRAPH_AWARE_TOOLS is not present in the current code", "Pre-dispatch interception remains the correct insertion point", "The MEMORY_AWARE_TOOLS defensive double-check pattern still exists", "The 250ms latency budget still exists, but Promise.allSettled remains a future-facing recommendation"], "ruledOut": ["Treating proposed graph/CocoIndex auto-enrichment as already shipped", "Assuming WorkingSetTracker performs session-start graph preloading"], "focusTrack": "verification", "timestamp": "2026-03-31T23:15:00.000Z", "durationMs": 300000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:91:{"type":"iteration","run":82,"status":"complete","focus":"VERIFY performance analysis from iteration 070 against current timing code in shared.ts, compact-inject.ts, compact-merger.ts, and budget-allocator.ts","findingsCount":6,"newInfoRatio":0.68,"noveltyJustification":"This pass uncovered a major scope correction: the live PreCompact hook only times stdin parsing and merge execution, so iteration 070's end-to-end headroom and enriched-pipeline latency numbers are not currently measured facts but mostly future-state estimates.","keyQuestions":["Which iteration 070 performance claims are still directly supported by current timing code?"],"answeredQuestions":["HOOK_TIMEOUT_MS is still 1800ms but only wraps parseHookStdin() in the live PreCompact hook","Token estimation still uses Math.ceil(text.length / 4)","Current code does not instrument or execute the richer SQLite/CocoIndex/tree-sitter hook pipeline assumed in iteration 070","Budget allocator timing remains uninstrumented"],"ruledOut":["Treating the 1800ms timeout as an end-to-end guard on the full live hook body","Treating 1-hop SQLite, CocoIndex, and full hook-path latency numbers as currently measured in source","Treating the current hook's cocoIndex section as a live CocoIndex MCP result"],"focusTrack":"verification","timestamp":"2026-03-31T13:38:38.148Z","durationMs":420000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:95:{"type":"iteration","run":86,"status":"complete","focus":"COPILOT CLI DEEP DIVE — instruction auto-loading, recovery reuse, and session-start auto-trigger design for memory_context + code_graph_scan","findingsCount":6,"newInfoRatio":0.71,"noveltyJustification":"This pass adds four concrete corrections to prior runtime assumptions: official Copilot CLI auto-loads AGENTS.md/.github/copilot-instructions.md/.github/instructions rather than a .github/copilot/ directory, repository-level custom agents live under .github/agents, repo-local .agents/agents is not the authoritative startup surface, and the right place for session-start graph priming is shared instruction files rather than optional agent profiles. Two findings deepen prior work by translating Claude recovery steps into Copilot-safe trigger patterns and by separating semantic vs structural auto-triggers.","keyQuestions":["Does Copilot CLI auto-load any instruction files?","How should Copilot auto-trigger memory_context and code_graph_scan on session start?","How does Copilot's markdown agent model change integration versus Codex TOML agents?"],"answeredQuestions":["Copilot CLI auto-loads AGENTS.md, .github/copilot-instructions.md, .github/instructions/**/*.instructions.md, optional root CLAUDE.md/GEMINI.md, and local/home instruction files","This repo currently has no .github/copilot/ directory or Copilot instruction files; the existing universal AGENTS.md already supplies Gate 1 memory_match_triggers but not code-graph startup priming","Copilot session-start priming should live in AGENTS.md plus optional .github/copilot-instructions.md or path-specific instructions, with code_graph_scan gated by code_graph_status and structural-intent triggers rather than fired on every turn","Copilot's markdown agent profiles are selection/delegation surfaces, whereas Codex TOML agents are canonical runtime prompts in this repo, so global startup behavior should not rely on Copilot agent profiles alone"],"ruledOut":["Using .github/copilot/ as the primary Copilot CLI auto-load surface","Relying on optional Copilot agent profiles alone for universal session-start priming","Running code_graph_scan unconditionally on every Copilot prompt"],"focusTrack":"non-hook-runtime","timestamp":"2026-03-31T13:49:25.654Z","durationMs":900000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:96:{"type":"iteration","run":85,"status":"complete","focus":"CODEX CLI deep dive — Session Start Protocol and @context auto-triggers","findingsCount":6,"newInfoRatio":0.83,"noveltyJustification":"4 of 6 findings are fully new (exact Codex agent inventory, cross-agent hook-wording audit, @context sequencing gap, and concrete CODEX.md/@context instruction text), while 2 deepen earlier non-hook-runtime findings about CODEX.md recovery behavior and Codex's lack of automatic graph warmup.","keyQuestions":["How should CODEX.md force memory_context() and code_graph_status() at session start?","What exact instruction additions should be made to .codex/agents/context.toml?"],"answeredQuestions":["A mandatory first-turn CODEX.md Session Start Protocol should call memory_context() and code_graph_status() before substantive work","The @context agent should gain a first-turn SESSION PRIME step, explicit code_graph_status() in its default sequence, and a structural auto-trigger subsection"],"ruledOut":["Relying on Claude-style SessionStart hooks in Codex","Forcing code_graph_scan() on every session start","Limiting the change to @deep-research only"],"focusTrack":"non-hook-runtime","timestamp":"2026-03-31T13:49:18.884Z","durationMs":480000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:97:{"type": "iteration", "run": 84, "status": "complete", "focus": "OPENCODE DEEP DIVE - concrete auto-trigger instructions for code graph + memory_context on session start", "findingsCount": 7, "newInfoRatio": 0.71, "noveltyJustification": "5 of 7 findings are fully new (complete OpenCode agent inventory with explicit MCP-binding audit, exact resume YAML injection point, per-agent insertion map, reusable OpenCode Session Start Protocol block, and concrete CLAUDE.md row/section rewrite). 2 findings are partially new because they refine prior non-hook-runtime work with direct current-code verification (scattered hook-aware fallback clauses and the minimal-friction split between graph status and graph expansion).", "keyQuestions": ["What exact OpenCode instruction changes should auto-trigger memory_context and code graph readiness on session start?"], "answeredQuestions": ["Which .opencode/agent files exist and which declare explicit MCP frontmatter bindings?", "Where is the best injection point in spec_kit_resume_auto.yaml for graph readiness?", "What universal Session Start Protocol should CLAUDE.md add?"], "ruledOut": ["auto-calling code_graph_context on every session start", "keeping graph startup logic only in late hook-routing appendices", "requiring Claude-style lifecycle hooks for OpenCode"], "focusTrack": "session-start-ux", "timestamp": "2026-03-31T13:58:00.000Z", "durationMs": 1500000}
.opencode/specs/system-spec-kit/024-compact-code-graph/research/deep-research-state.jsonl:100:{"type": "iteration", "run": 91, "status": "complete", "focus": "VERIFY review P1-10 and key P2 findings against current code (rootDir validation, compact cache freshness, workingSet reachability, transcript cache accounting, exception text exposure)", "findingsCount": 5, "newInfoRatio": 0.67, "noveltyJustification": "This pass fully revalidated the headline security and correctness findings against current source and added two important nuances: the startup Working Memory branch is unreachable through the normal hook pipeline rather than logically impossible, and cache buckets are parsed correctly but dropped only from surfaced totals and cost estimates.", "keyQuestions": ["Do review findings P1-10, P2-1, P2-2, P2-3, and P2-8 still match the current implementation?"], "answeredQuestions": ["code_graph_scan still accepts caller-controlled rootDir with no workspace-boundary validation", "session-prime still reuses pendingCompactPrime without any freshness check", "the startup Working Memory branch still has no in-repo workingSet producer", "transcript totals and surfaced USD estimates still exclude cacheCreation and cacheRead buckets", "memory_context and code_graph_context still reflect raw internal exception text back to callers"], "ruledOut": ["Treating session-stop's duplicate-save age check as protection for compact recovery freshness", "Treating the Working Memory branch as produced anywhere in the current hook pipeline", "Treating cache buckets as absent from transcript parsing"], "focusTrack": "verification", "timestamp": "2026-03-31T14:02:59.560Z", "durationMs": 900000}
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/079-speckit-cognitive-memory/plan.md:256:5. Verify with `memory_search` test query
.opencode/specs/system-spec-kit/024-compact-code-graph/review/review-report.md:21:- `P2-003` Session-resume public mirrors describe the legacy path: the feature catalog and manual playbook still tell operators to validate a `memory_context(mode=resume, profile=resume)` sub-call and an `ok|empty|error` graph-status contract, while the live handler uses the resume ladder and returns `fresh|stale|empty|error` [SOURCE: .opencode/skills/system-spec-kit/feature_catalog/22--context-preservation-and-code-graph/18-session-resume-tool.md:14] [SOURCE: .opencode/skills/system-spec-kit/manual_testing_playbook/22--context-preservation-and-code-graph/263-session-resume.md:17] [SOURCE: .opencode/skills/system-spec-kit/manual_testing_playbook/22--context-preservation-and-code-graph/263-session-resume.md:25] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:423] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:443].
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_10-53__full-spec-doc-indexing.md:452:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "../.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing" })` |
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_10-53__full-spec-doc-indexing.md:464:memory_search({ specFolder: "../.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_10-53__full-spec-doc-indexing.md:470:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_10-53__full-spec-doc-indexing.md:479:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:90:### CocoIndex Integration
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:92:CocoIndex Code MCP (existing, deployed) can enrich the PreCompact precomputation:
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:93:- **Semantic neighbors**: Query CocoIndex for code semantically related to active symbols/files from the session
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:94:- **Complements structural context**: While Memory MCP provides session/constitutional context, CocoIndex provides code-relevance context
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:95:- **Optional enrichment**: If CocoIndex is available, query `mcp__cocoindex_code__search` with active file/symbol context; if unavailable, proceed without (graceful degradation)
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:96:- **Budget impact**: CocoIndex results share the 4000-token compaction budget with memory results
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:106:| CocoIndex | 900 | Medium — semantic neighbors | 3rd |
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:113:- CocoIndex snippets trimmed to ≤600 chars (~175-225 tokens each)
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:123:| CocoIndex search | 450-700ms | 800ms |
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:137:     - Optionally queries CocoIndex for semantic neighbors of active symbols
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/spec.md:180:4. If no cache: call `memory_context({ mode: "resume" })` as fallback
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:4:Design a concrete "stale-on-read" mechanism for the code graph system. Building on iterations 59 (auto-reindex triggers) and 63 (stale detection), this iteration performs deep source code analysis of the existing content_hash and freshness mechanisms to design a file-watcher-free, on-demand staleness detection and auto-reindex system that integrates with both code_graph_query and code_graph_context call paths, plus CocoIndex coordination.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:68:### 7. CocoIndex freshness coordination design
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:69:CocoIndex has its own `ccc_reindex` tool and `refresh_index` management. The two systems can coordinate without coupling:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:71:**Independent refresh, shared trigger**: When the code graph's stale-on-read detects stale files, it can fire a lightweight event/flag that the next CocoIndex query checks. Concretely:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:74:- This avoids tight coupling: code graph triggers its own reindex synchronously; CocoIndex gets a hint to refresh incrementally
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:76:**Session-start batch**: On first MCP tool call of a session (detected via `resolveTrustedSession` from iteration 062), trigger both code graph scan and CocoIndex reindex in parallel. This is the "batch reindex on session start" from the dispatch brief:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:158:- Questions addressed: Auto-indexing design, staleness detection, latency impact, CocoIndex coordination, session-start batch reindex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-067.md:159:- Questions answered: Complete stale-on-read mechanism design with per-file granularity, concrete function signatures, schema extension, latency thresholds, and CocoIndex coordination strategy
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/plan.md:77:   - Optionally query CocoIndex for semantic neighbors of active files/symbols (if MCP available)
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/plan.md:103:- CocoIndex: 900 tokens floor (snippets trimmed to ≤600 chars)
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_08-38__full-spec-doc-indexing.md:477:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/z_archive/009-full-spec-doc-indexing" })` |
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_08-38__full-spec-doc-indexing.md:489:memory_search({ specFolder: "system-spec-kit/z_archive/009-full-spec-doc-indexing", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_08-38__full-spec-doc-indexing.md:495:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/009-full-spec-doc-indexing/scratch/legacy-memory-quarantine/16-02-26_08-38__full-spec-doc-indexing.md:504:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:4:Investigate performance characteristics of proposed improvements by analyzing the 1800ms hook timeout budget, SQLite query latency, token estimation accuracy, and CocoIndex search latency. Design a latency budget for the full auto-enrichment pipeline.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:47:### 6. CocoIndex Search Latency: MCP Roundtrip, Estimated 100-500ms
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:48:CocoIndex is an external MCP server (`mcp__cocoindex_code__search`). The latency includes:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:55:This is **not usable within the 1800ms hook budget** alongside other operations because CocoIndex requires an active MCP connection that hooks cannot assume. Hooks run as standalone Node.js processes (`process.exit(0)`) without MCP client connections. CocoIndex enrichment must be deferred to tool-dispatch-time or session-start priming via the MCP server context.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:56:[INFERENCE: based on MCP architecture (IPC pipe transport) and typical embedding model latency; CocoIndex runs as separate MCP server per .mcp.json configuration]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:95:| 4 | CocoIndex search (if applicable) | 100-500 | MCP roundtrip, parallel with #3 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:97:| **Total (without CocoIndex)** | | **~3-26ms** | Well under 250ms budget |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:98:| **Total (with CocoIndex)** | | **~103-526ms** | Needs async/timeout guard |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:102:2. CocoIndex MUST NOT be called in hook path (no MCP connection available)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:103:3. In MCP tool path, CocoIndex should run in parallel with graph queries, with a 250ms timeout
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:108:- CocoIndex in hook path: hooks run as standalone processes without MCP client connections; impossible to call MCP tools
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:125:- Questions answered: Hook budget headroom, SQLite query costs, token estimation accuracy, CocoIndex latency characteristics, tree-sitter parse times, pipeline latency budget design
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-070.md:129:- What did not work and why: CocoIndex latency is estimated rather than measured because it requires an active MCP connection; however, the architectural constraint (no MCP in hooks) makes exact measurement unnecessary for hook-path design.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-036.md:17:   | GitHub Copilot | Layered prompt assembly: system/custom instructions, conversation, implicit editor context, explicit refs, tool outputs, and workspace indexing | Hybrid: implicit local context + indexed retrieval + tools | Indirectly yes via repository indexing and code search, but public docs emphasize embeddings and indexing more than graph traversal | Exact retrieval budget not public |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-002.md:22:- **L1 Orchestration:** `memory_context`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-002.md:23:- **L2 Core:** `memory_search`, `memory_quick_search`, `memory_match_triggers`, `memory_save`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-002.md:99:- `memory_context` exposes a `resume` mode and supports a server-issued `sessionId`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-002.md:100:- `memory_search` supports session deduplication and optional session-based score boosts
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-002.md:101:- `memory_match_triggers` supports `session_id`, `turnNumber`, attention decay, tiered HOT/WARM injection, and co-activation
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-104.md:20:OpenCode has strong custom-agent infrastructure, but no documented zero-touch session-priming mechanism. That means context recovery currently depends on either the user/LLM manually invoking `@context` or `/spec_kit:resume`, or on the model remembering first-turn instructions like `memory_context(...resume...)` and `code_graph_status()`. [SOURCE: .opencode/commands/spec_kit/resume.md:1-17]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-104.md:26:- Description: Create a new `.opencode/agents/context-prime.md` as a narrow bootstrap agent. Its job would be: `memory_context({ input: "resume previous work continue session", mode: "resume", profile: "resume" })`, `code_graph_status({})`, optionally `ccc_status()`, then return a short "Prime Package" with active spec folder, current task, blockers, next steps, and retrieval-health status. This works with the existing custom-agent system because OpenCode already supports new agent files plus manual `@agent_name` invocation.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-104.md:45:- Dependencies: command runner, memory/code-graph/CocoIndex tools
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-104.md:70:| Copilot CLI | Instruction-driven first-turn recovery (`memory_context` + `code_graph_status`) | Can mirror `@context-prime` guidance, but no native startup hook | ~75% -> ~80% if mirrored |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-104.md:78:3. Make its output a compact "Prime Package": spec folder, current task, blockers, next steps, graph status, CocoIndex status.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:13:   The currently inspected production wiring updates `activeGoal` and `preferredAnchors` during `memory_search`, then applies `refineForGoal()`. In other words: what is live today is "query/result state", not "code artifact state". [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:690-705`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:21:   Iteration 045 already established the right preservation unit: a ranked structural working set built from "what the AI touched", plus nearby dependencies and verification surfaces. That aligns with DR-010, which explicitly separates CocoIndex as the semantic layer from code graph as the structural layer: semantic seeds first, structural expansion second. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:9-15`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:17-26`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:94-105`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:23:   Concretely, the graph's job here is not broad code search. Its job is: given touched files or symbols, recover the directly adjacent implementation surface the model will probably need next, such as imports, exports, callers, callees, tests, and config/runtime wiring.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:67:   This recommendation also fits the current architecture. `context-server.ts` already recognizes compaction-lifecycle `memory_context(mode:"resume")` calls, and `autoSurfaceAtCompaction()` already expects a bounded session-context summary with a 4,000-token budget. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:328-356`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:286-316`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:58-74`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:115:9. CocoIndex relevance scores should be used as a semantic boost on top of structural ranking, not as the primary definition of the working set.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:117:   DR-010 is explicit: CocoIndex handles semantic code search; code graph handles structural relationships; the intended enrichment flow is CocoIndex seeds followed by code-graph structural expansion. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:94-105`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:132:   Recommendation: use CocoIndex only after structural expansion, to rerank within the candidate neighborhood. "Structurally adjacent and semantically relevant" should rank highest; "structurally adjacent but semantically cold" should still beat "semantically similar but structurally distant" for compaction continuity.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:148:   - `semanticScore` or `semanticBoost` when CocoIndex is applied
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:181:Iteration 045 already established that compaction should preserve a ranked structural working set and that CocoIndex and code graph should remain complementary. The new contribution here is narrower and more implementation-facing: it maps that architecture onto the actual session mechanisms already in the repo. Specifically, this iteration distinguishes retrieval session state from persisted memory attention state, shows that neither currently captures code artifacts, defines the structural working set as seeds plus 1-hop neighbors, recommends a hybrid maintenance model (incremental seed logging plus on-demand graph expansion), and proposes the metadata and ranking policy needed to feed a compaction brief without overloading the existing `working_memory` system.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:189:5. Rank candidates with a composite score: edit strength, explicit mention, graph proximity, verification coupling, and CocoIndex semantic boost.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-053.md:192:8. Keep CocoIndex and code graph separate by role: semantic candidate seeding vs structural neighborhood expansion.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:11:   The existing server already uses a layered shape: `memory_context` is the orchestration entry point, `memory_search` and `memory_match_triggers` are focused retrieval tools, and `memory_index_scan` / ingest tools handle maintenance. The code graph should mirror that mental model instead of introducing a one-off "do everything" endpoint. The recommended public surface is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:135:   This is consistent with the current server shape. `memory_context` is already the start-here tool for intent-aware retrieval, while the search subsystem remains multi-channel and profile-aware. The code graph should become a sibling structural provider that can be fused with memory when the task is code-centric. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:39-187`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/README.md:1515-1547`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:139:   - `memory_context` stays the canonical top-level retrieval API for the overall system
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:140:   - `code_graph_context` is called directly for code-structure questions or internally by `memory_context` when the prompt mentions files, symbols, stack traces, call chains, or refactor intent
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:264:   The key schema choice is that `code_graph_query` should be explicit and deterministic, while `code_graph_context` can accept natural language and perform orchestration. This mirrors `memory_search` versus `memory_context`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:39-213`] [SOURCE: https://modelcontextprotocol.io/specification/2025-06-18/server/tools]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:369:- Existing server tool layering and "start with memory_context" contract:
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:63:| `:674` | `**Symptom:** memory_match_triggers() doesn't return your memory` | `**Symptom:** memory_match_triggers() doesn't return your constitutional rule` | Diagnostic row about constitutional-tier triggers. |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:118:| `context.md`, `deep-research.md`, `deep-review.md`, `orchestrate.md`, `review.md` | Each agent definition references `memory_context()` / `memory_search()` / `memory_match_triggers()` in workflow prose ("Do NOT redundantly call \`memory_context\` …"). Tool names stay verbatim (REQ-001). Surrounding prose ("memory operations" / "your memory" / "the memory system") gets the standard rewrite. | Apply vocabulary-key replacements to surrounding prose; leave backtick-quoted tool names alone. |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:122:The playbook scenarios script tool calls (e.g., "run `memory_search('semantic search')`"). Tool calls stay literal. Prose around them ("Verify that recent memories are returned") gets re-phrased per vocabulary key. ~62 occurrences, mostly mechanical.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:132:| `memory_context` (`:48`) | `[L1:Orchestration] Unified entry point for context retrieval with intent-aware routing. START HERE for most memory operations. […]` | `[L1:Orchestration] Unified entry point for spec-doc continuity retrieval with intent-aware routing. START HERE for most context-retrieval operations across indexed spec docs and constitutional rules. […]` |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:133:| `memory_search` (`:55`) | `[L2:Core] Search conversation memories semantically using vector similarity. Returns ranked results with similarity scores. Constitutional tier memories are ALWAYS included at the top of results (~2000 tokens max), regardless of query. […]` | `[L2:Core] Search the indexed spec-doc continuity store semantically using vector similarity. Returns ranked records (one record = one indexed spec-doc surface) with similarity scores. Constitutional tier rules are ALWAYS included at the top of results (~2000 tokens max), regardless of query. […]` |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:134:| `memory_search` `sessionId` param (`:81`) | `Session identifier for working memory and session deduplication (REQ-001). When provided with enableDedup=true, prevents duplicate memories from being returned in the same session (~50% token savings on follow-up queries).` | `Session identifier for working-memory cache and session deduplication (REQ-001). When provided with enableDedup=true, prevents duplicate spec-doc records from being returned in the same session (~50% token savings on follow-up queries).` |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:135:| `memory_search` `enableDedup` param (`:86`) | `Enable session deduplication (REQ-001). When true and sessionId provided, filters out already-sent memories.` | `Enable session deduplication (REQ-001). When true and sessionId provided, filters out already-sent spec-doc records.` |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:136:| `memory_search` `includeContiguity` param (`:91`) | `Include adjacent/contiguous memories in results` | `Include adjacent/contiguous spec-doc records in results (records from the same packet, neighboring sections)` |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:137:| `memory_search` `includeConstitutional` param (`:95`) | `Include constitutional tier memories at top of results (default: true)` | `Include constitutional tier rules at top of results (default: true)` |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:139:| `memory_match_triggers` description | (similar pattern) | "Match trigger phrases against indexed spec-doc records and surface the matching records (no embedding round-trip)" |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:154:### B2.1 `memory_context` and `memory_search` result formatters
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/phrasing-audit.md:190:| MCP tool names | `memory_search`, `memory_save`, `memory_context`, `memory_match_triggers`, `memory_index_scan`, all 21 | UNCHANGED |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/decision-record.md:168:- Folder rename would propagate to 30+ import paths, vitest test fixtures, and CocoIndex search index entries
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-015.md:28:- All runtimes get tool-based fallback via `memory_match_triggers()` and `memory_context({ mode: "resume" })`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-015.md:89:| 6. Session resume after crash/exit | `resetInterruptedSessions()` + `memory_context(resume)` + `CONTINUE_SESSION.md` | real SQLite fixture tests, resume/recovery integration tests | interrupted sessions become recoverable, resume reuses effective session, continuation artifact contains correct next step |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-015.md:149:- `memory_context()` already computes token-pressure decisions using a caller-provided `tokenUsage` ratio plus runtime token budget metadata.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-015.md:339:3. `memory_context()` can consume the latest session ratio without breaking existing telemetry shape.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/spec.md:80:- `tool-schemas.ts:48` (`memory_context` description) — "START HERE for most **memory operations**" — sent to AI agents on every tool list; the agent has to infer what "memory operations" means.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/spec.md:100:- **(B2) Runtime output strings** — formatter messages in `mcp_server/handlers/memory-*.ts` and `mcp_server/lib/.../formatters/*.ts` that produce text the user sees when a tool runs. Example: when `memory_context` returns "Loaded 3 memories", the message should name the 3 spec docs / packets it actually loaded.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/spec.md:104:- **Tool, command, frontmatter, table, file, and folder names** — `memory_search`, `memory_save`, `/memory:save`, `/memory:learn`, `_memory.continuity`, `memory_index` SQL table, `memory-search.ts` handler files, `references/memory/` folder, `scripts/dist/memory/` folder — all stay exactly as-is. The prior research output (archived) recommended a rename; the user explicitly scoped that out.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/spec.md:134:| REQ-003 | Runtime output messages from MCP tool handlers name specific spec folders, files, or counts when applicable. "Loaded 3 memories" becomes "Loaded 3 spec-doc records: implementation-summary.md from packet A, decision-record.md from packet B, …" or equivalent. | When `memory_context()` / `memory_search()` / `memory_save()` returns successfully, its output contains at least one of: a packet path, a doc filename, an explicit record count + source folder. |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/spec.md:179:**Given** an AI agent lists available MCP tools, **when** it reads `memory_search`'s `description:` string, **then** the description names the corpus searched (indexed spec docs + constitutional rules) rather than "conversation memories".
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/spec.md:181:**Given** an operator runs `memory_context()`, **when** the tool returns successfully, **then** the response message names the actual packets / docs that were loaded (e.g., "Loaded 3 spec-doc records from packets `026-...` and `023-...`") rather than "Loaded 3 memories".
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-035.md:14:1. The packet is implementation-capable at the core MCP layer, but only Phases 1-3 have enough technical specificity to start coding immediately; Phases 4-7 are progressively more dependent on unresolved contract and scope decisions. The strongest current implementation base is that `autoSurfaceAtCompaction()` already exists, `memory_context(mode:"resume")` is already treated as a compaction lifecycle call, and the response formatter already supports `profile: "resume"`, so the core retrieval primitives are real rather than hypothetical. The missing part is the transport adapter layer: `.claude/settings.local.json` currently contains no hook registrations, the Claude hook directories do not exist yet, `.claude/CLAUDE.md` is absent, and `CODEX.md` is absent. [Sources: `.opencode/specs/system-spec-kit/024-compact-code-graph/spec.md:40-45`, `.opencode/specs/system-spec-kit/024-compact-code-graph/plan.md:24-33`, `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:300-317`, `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:327-339`, `.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:418-424`, `.claude/settings.local.json:1-14`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-035.md:34:5. The research questions in `research.md` that remain unanswered are all still open, and they are currently misaligned with the hook-system phases: expected performance gain from a code graph channel, tree-sitter performance on this repo, whether code graph should be an MCP tool or background indexer, and whether CocoIndex should share the index. None of those questions are resolved by the current phase packet because the current packet is not actually about tree-sitter/code graph anymore. That mismatch should be resolved before further deep-research iterations continue, otherwise later iterations risk mixing two separate implementation tracks. [Sources: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:178-184`, `.opencode/specs/system-spec-kit/024-compact-code-graph/spec.md:17-45`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-035.md:48:  - `context-server.ts` already treats `memory_context(mode:"resume")` as a compaction lifecycle call. [Source: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:327-339`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-035.md:53:  - Root `CLAUDE.md` currently points resume work to `memory_context(... mode:"resume" ...)` but does not define the stronger compaction-recovery behavior proposed in Phase 4. [Source: `CLAUDE.md:49-51`]
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/079-speckit-cognitive-memory/001-analysis-cognitive-memory-systems.md:124:├─► search() → Hybrid (FTS5 + vector + RRF)
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:17:- Resume previous work should use `/spec_kit:resume` or `memory_context({ input: "resume previous work continue session", mode: "resume", specFolder })`. [SOURCE: `CLAUDE.md:51-51`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:38:`memory_context` has a dedicated `resume` mode with strategy `resume` and a 1200-token budget. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:581-587`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:42:`context-server.ts` treats `memory_context` with `args.mode === "resume"` as a "compaction lifecycle call" and routes it through `autoSurfaceAtCompaction(contextHint)` before normal dispatch. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:324-338`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:44:Tests confirm that runtime behavior: resume-mode `memory_context` invokes `autoSurfaceAtCompaction`, while non-resume `memory_context` uses the normal memory-aware path instead. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:965-997`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:56:### 3. `memory_context({ mode: "resume" })` is basically a tuned `memory_search`, not a special recovery object by default
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:137:The biggest gap is naming versus reality. `autoSurfaceAtCompaction()` sounds like a hook that fires when the client compacts context, but in the current implementation it only runs when **our own MCP server later receives** `memory_context(..., mode: "resume")`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/context-server.ts:326-338`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:141:- if the user or assistant never calls `/spec_kit:resume` or `memory_context(mode: "resume")`, nothing auto-surfaces
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:165:- **Documented recovery exists** via `/spec_kit:resume` and `memory_context(mode: "resume")`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-012.md:182:- Live MCP lookup via the in-session memory and CocoIndex tools did not return usable results here, so this iteration is based on source and test inspection rather than live tool responses. [CITATION: NONE]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-064.md:16:| code_graph_context accepts CocoIndex seeds (iter 054) | Seed resolution discards CocoIndex similarity score; needs near-exact tier (iter 059, 063) | **Deepened** — design gap at integration seam |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-064.md:44:| CocoIndex availability detection at runtime | Low | iter 059, 062 | Partial — ccc_status check mentioned but no graceful degradation path |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-064.md:58:| **P1-3** | Near-exact seed resolution + score propagation | 7/10 — bridges CocoIndex to code graph | ~60-80 LOC, low risk | **High** | seed-resolver.ts exists | iter 059, 063 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-064.md:67:| **P3-2** | ccc_feedback implicit positive feedback | 3/10 — CocoIndex quality improvement | ~30-50 LOC, low risk | **Moderate** | ccc_feedback API exists | iter 059 |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-064.md:85:5. **"CocoIndex and Code Graph are independent" (iter 051)** — Partially revised. They are independent at the index level (no shared event bus), but at the query level they benefit from tighter integration: score propagation, near-exact seed resolution, hybrid query patterns. The relationship is "loosely coupled indexes, tightly integrated queries."
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-064.md:89:1. **"CocoIndex covers semantic, code graph covers structural"** (iter 036-045) — Fully reinforced. No segment 6 finding suggests overlap or redundancy.
.opencode/specs/system-spec-kit/z_archive/012-spec-doc-anchor-tags/scratch/legacy-memory-quarantine/16-02-26_14-12__spec-doc-anchor-tags.md:503:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/z_archive/012-spec-doc-anchor-tags" })` |
.opencode/specs/system-spec-kit/z_archive/012-spec-doc-anchor-tags/scratch/legacy-memory-quarantine/16-02-26_14-12__spec-doc-anchor-tags.md:515:memory_search({ specFolder: "system-spec-kit/z_archive/012-spec-doc-anchor-tags", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/012-spec-doc-anchor-tags/scratch/legacy-memory-quarantine/16-02-26_14-12__spec-doc-anchor-tags.md:521:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/012-spec-doc-anchor-tags/scratch/legacy-memory-quarantine/16-02-26_14-12__spec-doc-anchor-tags.md:530:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/deep-research-strategy.md:18:- **Per iteration:** @deep-research reads Next Focus, runs 3–5 research actions (WebFetch + Grep + Read + memory_search), writes iteration-NNN.md. Reducer refreshes machine-owned sections.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/deep-research-strategy.md:318:memory_context() at session init returned no directly-matching results for "memory terminology rename system-spec-kit MCP tool naming spec-doc continuity" (`focused` mode, `understand` intent, token budget 3000). Auto-surfaced triggered memories pointed at adjacent prior work but none re-solve the present problem:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-097.md:10:`compact-inject.ts` tails the last ~50 transcript lines, extracts active files, topics, spec folder, and "attention" identifiers, runs `mergeCompactBrief`, optionally auto-surfaces constitutional memories, then caches the payload as `pendingCompactPrime` in hook state for the Claude session. `session-prime.ts` reads and clears that cache on `source=compact`, injects the recovered brief, and still tells the model to call `memory_context({ mode: "resume", profile: "resume" })` for full state.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-097.md:12:Non-hook CLIs lack that event. They only have manual doc instructions plus generic MCP continuity primitives: `memory_context` resume mode, trusted `effectiveSessionId`, working-memory event counters, inferred mode, and persisted session identity in `session-manager`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-097.md:24:- Description: Add a `session_health` tool/endpoint that scores likely context continuity using existing MCP-side signals: trusted `effectiveSessionId`, event counter continuity, last session-state update, working-memory prompt context availability, token-pressure ratio, and elapsed wall-clock gap since last tool call. Return `ok | warning | stale` plus recovery hints and a recommended next action (`memory_context` resume, re-read runtime doc, inspect spec folder).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-097.md:58:- Description: When MCP sees a suspicious gap before the next tool call, inject a recovery payload into the next tool response envelope metadata/hints. This is the closest non-hook analogue to Claude's post-compaction injection. Trigger on elapsed gap, session mismatch, empty working-memory context after a previously active session, or sudden reset-like query patterns ("where was I", "resume", repeated onboarding questions). Payload should include last spec folder, last task, checkpoint freshness, and a one-line instruction to call `memory_context(...resume...)`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-097.md:72:- Description: Strengthen `CODEX.md`, `GEMINI.md`, `AGENTS.md`, and root `CLAUDE.md` so non-hook runtimes proactively self-check continuity. Add explicit triggers: after long tool streaks, after >15 minutes idle, after repeated "what next"/"where was I" prompts, after unusually generic user follow-up, or when prior file/spec references disappear from working context. Instruct the model to call `memory_context({ input: "resume previous work continue session", mode: "resume", profile: "resume" })` and optionally `session_health`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-097.md:111:3. Update runtime docs to call `session_health` + `memory_context(...resume...)` on explicit drift triggers.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/review/deep-review-strategy.md:74:- 21 MCP tool names: `memory_context`, `memory_search`, `memory_quick_search`, `memory_match_triggers`, `memory_save`, `memory_update`, `memory_delete`, `memory_list`, `memory_index_scan`, `memory_validate`, `memory_health`, `memory_stats`, `memory_bulk_delete`, `memory_get_learning_history`, `memory_drift_why`, `memory_causal_link`, `memory_causal_unlink`, `memory_causal_stats`, `memory_ingest_start`, `memory_ingest_status`, `memory_ingest_cancel`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-077.md:9:Current code does implement **memory** auto-surface at two lifecycle points: tool dispatch and compaction. `context-server.ts` runs a pre-dispatch auto-surface block, choosing either `autoSurfaceMemories` / `autoSurfaceAtCompaction` for memory-aware tools or `autoSurfaceAtToolDispatch` for other tools. `memory-surface.ts` only defines those two hook entry points. However, the inspected files do **not** implement a three-tier graph/CocoIndex enrichment stack with session lifecycle preloading, inline graph injection, and query-aware deferred graph enrichment. `WorkingSetTracker` only tracks, ranks, serializes, and deserializes file/symbol accesses; it does not preload graph context. In `session-prime.ts`, the working set is only rendered as a plain "Recently active files" list.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-077.md:32:The actual pure pass-through dispatcher is `dispatchTool()` in `tools/index.ts`, which loops over `ALL_DISPATCHERS` and forwards to the first matching tool module. `context-server.ts` wraps that dispatcher with the pre-dispatch auto-surface block before calling `dispatchTool(name, args)`. So the important conclusion from iteration 061 is still correct: interception for any future graph/CocoIndex auto-enrichment must happen in the **pre-dispatch block in `context-server.ts`**, not inside the dispatcher. The nuance is that the pass-through behavior lives in `tools/index.ts`, while `context-server.ts` is the orchestration layer around it.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-077.md:48:`context-server.ts` still measures auto-surface latency and warns when the precheck exceeds 250ms. But the current implementation only performs a **single** auto-surface path per call; there is no parallel graph+memory enrichment branch and no `Promise.allSettled` orchestration in the inspected files. So the latency constraint is real, but the claim that the system therefore "requires `Promise.allSettled`" should be treated as an implementation recommendation for a future graph/CocoIndex enrichment path, not a current fact.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-077.md:61:  - The three-tier graph/CocoIndex auto-enrichment architecture is not implemented in the current code.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-077.md:88:- What worked and why: Re-reading the live source made it easy to distinguish between **implemented memory auto-surface behavior** and **proposed graph/CocoIndex extension architecture**. The gap is not that the code changed dramatically; it is that earlier iterations blurred design proposals and current behavior.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:35:`context.md` already makes memory-first retrieval a hard habit: its core workflow starts with `memory_match_triggers -> memory_context -> memory_search`, and its tool sequence continues from memory into CocoIndex, Glob, Grep, and Read. Several other agents already mention Claude `SessionStart` hook context explicitly: `deep-research`, `deep-review`, `handover`, and `speckit` each say "if hook-injected context is present, use it; otherwise fall back to `memory_context({ mode: "resume", profile: "resume" })` then `memory_match_triggers()`". `orchestrate.md` has the same recovery ordering in its "Context Recovery Priority" section. The gap is that none of these first-turn recovery paths call `code_graph_status()` or `code_graph_scan()`, so code graph freshness is not part of session startup today.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:46:The best place to insert code-graph auto-triggering is `workflow.step_2_load_memory`, immediately after the existing `memory_context(mode: "resume")` recovery step and before the flow extracts the "Resume Essentials" packet. That keeps the current order intact: recover session continuity first, then check structural-index readiness before recommending a "next safe action". A secondary, presentation-only insertion point exists in `step_4_present_resume`, where the workflow can surface `graph_status: ready | reindexing | unavailable` alongside the resume brief.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:53:- `Research/exploration` -> `memory_match_triggers()` then `memory_context()` or `memory_search()`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:54:- `Code search` -> `CocoIndex search` -> `Grep()` -> `Glob()` -> `Read()`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:55:- `Resume prior work` -> `/spec_kit:resume` or `memory_context(... mode: "resume" ...)`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:57:Gate 1 also starts every new message with `memory_match_triggers(prompt)`. There is no Session Start Protocol section and no structural code-graph step in the current quick-reference workflow. In other words, the universal template currently covers continuity context and semantic search, but not structural-index readiness.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:74:1. `memory_match_triggers(prompt)`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:75:2. `memory_context({ input: prompt, mode: "auto" })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:76:3. If resuming known prior work, prefer `memory_context({ input: "resume previous work continue session", mode: "resume", profile: "resume", specFolder })`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:103:- always run `memory_context(...)` during recovery
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:119:| **Session start** | Hook context if present -> else `memory_match_triggers(prompt)` -> `memory_context(...)` -> `code_graph_status()` -> if stale and code-facing: `code_graph_scan({ incremental: true })` |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:125:| **Code search** | `code_graph_context()/code_graph_query()` for structural questions -> `CocoIndex search` for semantic/intent queries -> `Grep()` for exact text -> `Glob()` for file paths -> `Read()` for contents |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:143:- Requiring Claude-style lifecycle hooks for OpenCode. The existing OpenCode files already assume a non-hook fallback path (`memory_context` then `memory_match_triggers`), so the right upgrade is stronger self-trigger instructions, not a hook dependency. [SOURCE: .opencode/agents/orchestrate.md:807-812] [SOURCE: .opencode/agents/deep-research.md:439-441]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:167:  - What does `CLAUDE.md` currently say about code search and resume?
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-084.md:168:  - What exact OpenCode agent instruction changes should auto-trigger `memory_context` and `code_graph_scan`?
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:1:# Iteration 050: Compact Repo Map Generation — Structural Graph + CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:5:Determine how to generate compact, query-aware repository maps by combining two assets we now have: a structural code graph (tree-sitter + SQLite with nodes, edges, and files) and CocoIndex semantic search results. The goal is to move from "repo map as static outline" toward "repo map as a token-budgeted structural projection of the code most relevant to the current task." This iteration specifically answers how aider's repo-map works, how our typed graph improves on it, how CocoIndex should influence ranking, what output shape is best for LLMs, and what the right MVP is for `024-compact-code-graph`. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-032.md:9-45`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:155-246`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:94-105`] [SOURCE: https://aider.chat/docs/repomap.html] [SOURCE: https://aider.chat/2023/10/22/repomap.html]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:38:3. CocoIndex relevance should act as a query-conditioned prior that seeds and boosts the structural ranking, not as a replacement for it.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:41:   1. run CocoIndex on the current task/query to get the top semantic hits;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:47:   CocoIndex is the right recall engine because it retrieves by meaning; the graph is the right precision engine because it knows exact topology. Earlier packet work already established that CocoIndex chunks are structure-aware but not symbol-identical, so the correct bridge is "semantic hit overlaps node(s)," not "semantic chunk is the node." Recommended v1 scoring order is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:49:   - CocoIndex hit score on overlapping nodes,
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:55:   Practical recommendation: use CocoIndex as a bounded boost, not the dominant score. A semantically similar but structurally distant file should not outrank a direct caller, imported module, or failing test neighbor of the active symbol. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:95-105`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:28-40`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:96-118`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-047.md:7-23`] [SOURCE: `.opencode/skills/mcp-coco-index/references/settings_reference.md:144-159`] [SOURCE: `.opencode/skills/mcp-coco-index/references/tool_reference.md:266-272`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:88:   This preserves freshness, makes token budgeting query-specific, and allows CocoIndex to influence ranking in real time. A static precomputed repo map can still exist as a fallback project outline or cold-start aid, but it should not be the primary product because the whole point of combining graph + CocoIndex is task sensitivity. The graph index is the durable asset; the repo map is a just-in-time view over it. That mirrors the strongest part of aider's design while avoiding its limitation of collapsing structure too early. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-032.md:9-45`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-041.md:7-18`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:173-177`] [SOURCE: https://aider.chat/docs/repomap.html]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:92:   The packet already defined Tier A as 1K-4K tokens, which is broader than aider's typical 1K budget but fits our three-tier model. That range is still correct after combining structural graph and CocoIndex because the added value is better ranking, not radically larger payloads. Recommended sizing policy:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:114:8. The repo map should include structural signatures by default and CocoIndex-derived summaries only selectively.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:116:   Signatures, symbol kinds, export status, and typed neighbors should remain the default Tier A payload because they are stable, cheap, and grounded in the structural index. CocoIndex-generated natural-language summaries are useful, but only when they clarify why a symbol matters or when the symbol name/signature is too opaque. Good candidates are:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:122:   That means the map should not become a wall of summaries. Use structural signatures everywhere, and optionally add a terse "why this matters" note informed by CocoIndex relevance. This preserves scanability and avoids spending Tier A budget on prose that belongs in Tier B symbol summaries. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:202-217`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-039.md:24-60`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-047.md:7-23`] [SOURCE: `.opencode/skills/mcp-coco-index/references/settings_reference.md:144-159`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:135:   Between the two candidate MVPs, dynamic wins. A static structural outline would prove the graph exists, but it would not prove the graph plus CocoIndex combination is better than either system alone. The smallest useful MVP is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:138:   - optionally query CocoIndex for semantic seeds;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:144:   Keep a static package/file outline as a fallback when there is no query or when CocoIndex is unavailable, but the MVP should be query-ranked from day one. Otherwise we would be building only the "structural outline" half of the design and postponing the actual value of the hybrid. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/plan.md:93-106`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:95-105`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:50-58`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:177-209`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-047.md:45-70`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:179:This iteration is not a first-discovery pass; it is a synthesis pass that turns several previously separate findings into one implementation-ready repo-map design. The net-new value is the integration logic: treating aider as the projection baseline, the structural graph as the storage/ranking substrate, CocoIndex as the semantic prior, and the repo map itself as a dynamic Tier A view rather than a static outline or raw graph dump. The strongest new conclusions are that query-ranked dynamic maps should be the MVP, CocoIndex summaries should be selective rather than default, package-scoped maps should be the monorepo default, and semantic hits should map to structural nodes via overlap rather than identity.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:187:3. Add a bridge layer from CocoIndex hit spans to structural nodes using overlap/enclosing-node resolution; do not store semantic chunks as graph nodes.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:191:   - CocoIndex overlap boost,
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:206:10. Ship the MVP as a query-ranked dynamic map with static outline fallback. A static-only MVP would prove indexing but would not validate the structural-graph-plus-CocoIndex design that this packet is trying to establish.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:216:+# Iteration 050: Compact Repo Map Generation — Structural Graph + CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:220:+Determine how to generate compact, query-aware repository maps by combining two assets we now have: a structural code graph (tree-sitter + SQLite with nodes, edges, and files) and CocoIndex semantic search results. The goal is to move from "repo map as static outline" toward "repo map as a token-budgeted structural projection of the code most relevant to the current task." This iteration specifically answers how aider's repo-map works, how our typed graph improves on it, how CocoIndex should influence ranking, what output shape is best for LLMs, and what the right MVP is for `024-compact-code-graph`. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-032.md:9-45`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:155-246`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:94-105`] [SOURCE: https://aider.chat/docs/repomap.html] [SOURCE: https://aider.chat/2023/10/22/repomap.html]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:253:+3. CocoIndex relevance should act as a query-conditioned prior that seeds and boosts the structural ranking, not as a replacement for it.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:256:+   1. run CocoIndex on the current task/query to get the top semantic hits;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:262:+   CocoIndex is the right recall engine because it retrieves by meaning; the graph is the right precision engine because it knows exact topology. Earlier packet work already established that CocoIndex chunks are structure-aware but not symbol-identical, so the correct bridge is "semantic hit overlaps node(s)," not "semantic chunk is the node." Recommended v1 scoring order is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:264:+   - CocoIndex hit score on overlapping nodes,
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:270:+   Practical recommendation: use CocoIndex as a bounded boost, not the dominant score. A semantically similar but structurally distant file should not outrank a direct caller, imported module, or failing test neighbor of the active symbol. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:95-105`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:28-40`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:96-118`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-047.md:7-23`] [SOURCE: `.opencode/skills/mcp-coco-index/references/settings_reference.md:144-159`] [SOURCE: `.opencode/skills/mcp-coco-index/references/tool_reference.md:266-272`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:303:+   This preserves freshness, makes token budgeting query-specific, and allows CocoIndex to influence ranking in real time. A static precomputed repo map can still exist as a fallback project outline or cold-start aid, but it should not be the primary product because the whole point of combining graph + CocoIndex is task sensitivity. The graph index is the durable asset; the repo map is a just-in-time view over it. That mirrors the strongest part of aider's design while avoiding its limitation of collapsing structure too early. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-032.md:9-45`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-041.md:7-18`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:173-177`] [SOURCE: https://aider.chat/docs/repomap.html]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:307:+   The packet already defined Tier A as 1K-4K tokens, which is broader than aider's typical 1K budget but fits our three-tier model. That range is still correct after combining structural graph and CocoIndex because the added value is better ranking, not radically larger payloads. Recommended sizing policy:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:329:+8. The repo map should include structural signatures by default and CocoIndex-derived summaries only selectively.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:331:+   Signatures, symbol kinds, export status, and typed neighbors should remain the default Tier A payload because they are stable, cheap, and grounded in the structural index. CocoIndex-generated natural-language summaries are useful, but only when they clarify why a symbol matters or when the symbol name/signature is too opaque. Good candidates are:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:337:+   That means the map should not become a wall of summaries. Use structural signatures everywhere, and optionally add a terse "why this matters" note informed by CocoIndex relevance. This preserves scanability and avoids spending Tier A budget on prose that belongs in Tier B symbol summaries. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:202-217`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-039.md:24-60`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-047.md:7-23`] [SOURCE: `.opencode/skills/mcp-coco-index/references/settings_reference.md:144-159`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:350:+   Between the two candidate MVPs, dynamic wins. A static structural outline would prove the graph exists, but it would not prove the graph plus CocoIndex combination is better than either system alone. The smallest useful MVP is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:353:+   - optionally query CocoIndex for semantic seeds;
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:359:+   Keep a static package/file outline as a fallback when there is no query or when CocoIndex is unavailable, but the MVP should be query-ranked from day one. Otherwise we would be building only the "structural outline" half of the design and postponing the actual value of the hybrid. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/plan.md:93-106`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:95-105`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:50-58`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:177-209`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-047.md:45-70`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:394:+This iteration is not a first-discovery pass; it is a synthesis pass that turns several previously separate findings into one implementation-ready repo-map design. The net-new value is the integration logic: treating aider as the projection baseline, the structural graph as the storage/ranking substrate, CocoIndex as the semantic prior, and the repo map itself as a dynamic Tier A view rather than a static outline or raw graph dump. The strongest new conclusions are that query-ranked dynamic maps should be the MVP, CocoIndex summaries should be selective rather than default, package-scoped maps should be the monorepo default, and semantic hits should map to structural nodes via overlap rather than identity.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:402:+3. Add a bridge layer from CocoIndex hit spans to structural nodes using overlap/enclosing-node resolution; do not store semantic chunks as graph nodes.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:406:+   - CocoIndex overlap boost,
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:421:+10. Ship the MVP as a query-ranked dynamic map with static outline fallback. A static-only MVP would prove indexing but would not validate the structural-graph-plus-CocoIndex design that this packet is trying to establish.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-050.md:556:    - decision-record.md: Extra custom section header '## DR-010: CocoIndex as Complementary Semantic Layer' does not exist in the active template
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-010.md:42:All 10 strategy.md key questions are answered with primary-source citations across iter-1..iter-10. The vocabulary verdict is **single `continuity_*` axis** for L3-L5 surfaces, with L1 SQL tables staying `memory_*` (NO-ACTION), L2 markdown unchanged, L6 cognitive subsystem carving out FSRS + Miller's-Law loanwords. The deprecation alias matrix is 3-tier: T1 (4 tools — `memory_search`, `memory_context`, `memory_save`, `memory_index_scan`) permanent; T2 (4 tools) 2-release window; T3 (13 tools) 1-release window.
.opencode/specs/system-spec-kit/z_archive/010-documentation-alignment/scratch/legacy-memory-quarantine/16-02-26_11-43__spec126-documentation-alignment.md:445:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "../.opencode/specs/system-spec-kit/127-spec126-documentation-alignment" })` |
.opencode/specs/system-spec-kit/z_archive/010-documentation-alignment/scratch/legacy-memory-quarantine/16-02-26_11-43__spec126-documentation-alignment.md:457:memory_search({ specFolder: "../.opencode/specs/system-spec-kit/127-spec126-documentation-alignment", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/010-documentation-alignment/scratch/legacy-memory-quarantine/16-02-26_11-43__spec126-documentation-alignment.md:463:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/010-documentation-alignment/scratch/legacy-memory-quarantine/16-02-26_11-43__spec126-documentation-alignment.md:472:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/001-precompact-hook/implementation-summary.md:93:Floors + overflow pool model across 4 sources within the 4000-token compaction budget: Constitutional Memory (700 floor), Code Graph (1200 floor), CocoIndex (900 floor), Triggered Memory (400 floor), Overflow Pool (800 redistributed from empty sources).
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:9:That first-call `PrimePackage` is also fairly lightweight and mostly inferred from tool args, not persistent session state. It derives `specFolder` from `toolArgs.specFolder`, derives `currentTask` from `input/query/prompt`, infers graph freshness from the snapshot, detects CocoIndex availability, and emits recommended calls. It does **not** pull "last active spec folder" or "last task" from prior session memory. [SOURCE: `hooks/memory-surface.ts:315-363`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:51:- CocoIndex availability
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:147:- CocoIndex availability
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:149:  - "If resuming previous work, call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`."
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:183:Augment descriptions for tools like `memory_context`, `session_health`, `session_resume`, and maybe `memory_match_triggers` so that even if clients downplay server instructions, the model still sees strong affordances in tool metadata:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:250:- CocoIndex availability
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:272:- `memory_context`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-110.md:275:- `memory_match_triggers`
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/review/iterations/iteration-003.md:12:- `mcp_server/tool-schemas.ts` still declares 21 `memory_*` MCP tool names: `memory_context`, `memory_search`, `memory_quick_search`, `memory_match_triggers`, `memory_save`, `memory_list`, `memory_stats`, `memory_health`, `memory_delete`, `memory_update`, `memory_validate`, `memory_bulk_delete`, `memory_drift_why`, `memory_causal_link`, `memory_causal_stats`, `memory_causal_unlink`, `memory_index_scan`, `memory_get_learning_history`, `memory_ingest_start`, `memory_ingest_status`, `memory_ingest_cancel`.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/review/iterations/iteration-003.md:23:- `mcp_server/tool-schemas.ts:47-54` keeps tool names frozen while `memory_context` / `memory_search` descriptions point to spec-doc continuity retrieval and indexed spec-doc records.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/review/iterations/iteration-003.md:107:- `feature_catalog/feature_catalog.md:171-179` still references correct MCP tool names (`memory_context`, `memory_quick_search`, `memory_search`, `memory_save`, and related tools).
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/review/iterations/iteration-003.md:117:- `manual_testing_playbook/13--memory-quality-and-indexing/003-context-save-index-update.md:32-44` still validates generated context artifacts through `memory_search` / `memory_context` and tier-invariant spot checks.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-037.md:30:   - DFG is best for value tracking, variable misuse, semantic similarity, bug-finding, and code search where "what value reaches here?" matters.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-037.md:161:Earlier packet research already established that tree-sitter, aider-style repo maps, and CocoIndex are relevant building blocks. This iteration adds a broader research-layer synthesis that was not previously captured: a clear taxonomy of code graph types, a task-to-graph suitability map, a comparison of graph richness versus construction cost, an industry comparison across CodeQL/Semgrep/Sourcegraph, and a direct recommendation about which graph projections are compact enough for LLM consumption. The most important new conclusion is that the right design is not "full code property graph in prompt," but "rich graph in storage, compact graph projection for the model."
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-005.md:23:5. **Letta (formerly MemGPT) uses a 3-tier memory taxonomy: `core memory` / `recall memory` / `archival memory` — explicit per-tier naming with the "memory" suffix retained.** Letta's well-documented public taxonomy splits agent memory into: (1) **core memory** — always-in-context blocks; (2) **recall memory** — automatic conversation history with retrieval; (3) **archival memory** — explicit long-term knowledge store. Two relevant differentiators: (a) Letta retained the "memory" suffix because their entire product is positioned as a memory framework — they don't have our Anthropic-collision pressure; (b) Letta's tier names are NOT prefixes on tool names (their tools are `archival_memory_search`, `core_memory_append`, etc. — verb-modeled). **Implication**: our iter-2 finding 8 tier-stratified alias matrix is a *deprecation* tier, not a *retrieval* tier. Letta's 3-tier model is parallel evidence that 3-tier memory stratification is intuitive at the user level. [SOURCE: Letta public docs `docs.letta.com/concepts/memory`, iteration 5]
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/review/prompts/iteration-001.md:20:   - 21 `memory_*` MCP tools: memory_context, memory_search, memory_quick_search, memory_match_triggers, memory_save, memory_update, memory_delete, memory_list, memory_index_scan, memory_validate, memory_health, memory_stats, memory_bulk_delete, memory_get_learning_history, memory_drift_why, memory_causal_link, memory_causal_unlink, memory_causal_stats, memory_ingest_start, memory_ingest_status, memory_ingest_cancel
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/review/prompts/iteration-001.md:50:   grep -rn 'memory_search\|memory_save\|memory_context\|memory_match_triggers' .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts | wc -l
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-003.md:29:| **Context retrieval** | graph_continue, graph_read | memory_context, memory_search, memory_quick_search |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/spec.md:30:Phase 2 of `001-research-graph-context-systems` is a read-only audit of the codesight external Node.js/TypeScript skill (zero-runtime-dependency CLI that scans a project root and generates AI-assistant context artifacts) to translate its detector architecture, MCP tool design, profile generation, scanner heuristics, and blast-radius analysis into concrete improvements for `Code_Environment/Public`'s existing structural retrieval stack (Code Graph MCP, CocoIndex, Spec Kit Memory). The deliverable is an evidence-backed Adopt/Adapt/Reject table plus late-session adoption synthesis grounded in specific `external/src/` file:line citations across 20 deep-research iterations, not a generic feature inventory. No source files outside this spec folder are modified during the research phase.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/spec.md:60:`Code_Environment/Public` already has CocoIndex semantic search, Code Graph MCP for structural queries, and Spec Kit Memory for context preservation, but it lacks Codesight-style automated `CLAUDE.md` / `.cursorrules` / `codex.md` / `AGENTS.md` generation from a single project scan, per-AI-tool profile generation, and a blast-radius command built around reverse-import BFS. Without an evidence-grounded survey of Codesight's actual implementation (separated from its README marketing claims), any port would risk importing the wrong patterns, the wrong claims, and the wrong risks.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/spec.md:93:- Re-implementing CocoIndex semantic search, Code Graph MCP structural queries, or Spec Kit Memory in Public.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/spec.md:92:- Implementing runtime code in Spec Kit Memory, Code Graph, CocoIndex, or startup hooks.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-001.md:11:2. **Layer 1+5 (storage + retrieval pipeline) exposes 21 public `memory_*` MCP tools, not 9.** The spec.md §3 and strategy.md §12 both cite 9, but `tool-schemas.ts` enumerates 21: `memory_context`, `memory_search`, `memory_quick_search`, `memory_match_triggers`, `memory_save`, `memory_list`, `memory_stats`, `memory_health`, `memory_delete`, `memory_update`, `memory_validate`, `memory_bulk_delete`, `memory_drift_why`, `memory_causal_link`, `memory_causal_stats`, `memory_causal_unlink`, `memory_index_scan`, `memory_get_learning_history`, `memory_ingest_start`, `memory_ingest_status`, `memory_ingest_cancel`. This 2.3× undercount means the Q3 alias-window decision must price 21 deprecation aliases, not 9, and the REQ-008 advisor regression bundle has more trigger phrases to keep balanced than the spec assumes. The discrepancy is an actionable spec-error finding, not a research artifact. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:47, 54, 196, 214, 221, 228, 234, 240, 280, 295, 301, 323, 416, 423, 429, 435, 494, 500, 506, 529, 542]
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-001.md:17:5. **Anthropic's Claude Memory tool primary terminology is narrow and well-bounded.** Verbatim noun phrases used by Anthropic: "memory tool", "memory file directory", "memory directory", "memory operations", "memory commands" (the six are `view`, `create`, `str_replace`, `insert`, `delete`, `rename`), "memory artifacts", "memory store", "memory backend", "/memories" (the canonical container path), "memory_20250818" (the API beta tool type identifier), and "memory tool helpers". The conceptual layers are: (1) the LLM tool surface (`tools: [{type: "memory_20250818", name: "memory"}]`), (2) the client-side handler implementation (`BetaAbstractMemoryTool` / `betaMemoryTool`), and (3) the on-disk container (`/memories`). Anthropic does NOT use the terms `continuity`, `spec doc`, `packet`, `handover`, `recovery ladder`, `causal graph`, or `lineage` — none of our internal vocabulary collides downward. The collision surface is bidirectional and asymmetric: any of our identifiers that contain the bare token `memory` (especially `memory_save`, `memory_search`, `memory_context`, `memory_match_triggers`, `/memory:save`, `/memory:search`, `_memory.continuity`) will read in our READMEs as if they refer to Anthropic's tool. The reverse is not true — Anthropic's `memory_20250818` is dated and clearly Anthropic-branded. This means the rename's collision-mitigation work falls entirely on the local side; we do NOT need a defensive Anthropic-side disambiguation strategy beyond a one-line positioning callout. [SOURCE: https://platform.claude.com/docs/en/docs/agents-and-tools/tool-use/memory-tool]
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-001.md:27:| **L5: Hybrid retrieval pipeline** | 5-channel fusion (vector + BM25 + FTS + causal graph + degree) + CocoIndex bridge + 21 public `memory_*` tools | 21 MCP tools (all `memory_*`-prefixed), `mcp_server/lib/search/`, `mcp_server/lib/scoring/` | High (this is the user-facing surface; every README quoting `memory_search` or `/memory:search` reads like Anthropic's tool) | `continuity_*`, `recall_*`, `spec_doc_*`, `lookup_*`. Recommend `continuity_*` for retrieval/save tools; `recall_*` rejected as too cognitive-science |
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/02-01-26_14-09__generate-context-modularization.md:312:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/058-generate-context-modularization" })` |
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/02-01-26_14-09__generate-context-modularization.md:317:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-100.md:35:- No reliance on "remember to call `memory_context` first."
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-100.md:57:`AGENTS.md` already contains most of the universal framework, including session start for Copilot/Gemini, code search protocol, gates, memory-save rules, and runtime agent directory resolution. [SOURCE: AGENTS.md:44-230]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:8:2. CocoIndex: semantic code neighbors of the active working set
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:23:   - Stage 1b: run CocoIndex over active symbols/files in parallel
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:24:   - Stage 2: expand Code Graph from active symbols plus top CocoIndex hits used as structural seeds
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:27:   This is stronger than `Memory -> Code Graph -> CocoIndex` because the packet already says `code_graph_context` should accept CocoIndex results as seeds for structural expansion, and the revised compaction pipeline explicitly lists semantic retrieval before structural expansion. At the same time, Memory should still start immediately because the current hook guarantees constitutional+triggered surfacing and already has compaction-specific budget enforcement. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/plan.md:104-106`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:500-512`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:188-223`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:300-316`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:33:   If the same file or symbol appears in both CocoIndex and Code Graph, we should not print it twice in the final injected payload. Instead, the merge layer should produce one canonical candidate keyed by `symbolId` when available, or `filePath` as a fallback, with per-source provenance retained in the cached JSON. Code Graph should contribute structural rationale (`imported by`, `calls`, `tested_by`), while CocoIndex contributes semantic rationale (`matched active symbol`, `conceptual neighbor`). Iteration 044 strongly supports this because it requires stable node IDs, explicit file/range/signature metadata, and late fusion between memory and graph rather than store collapse. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:117-135`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:97:   1. Build the PreCompact fusion layer that merges Memory, CocoIndex, and Code Graph into one cache file.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:115:     Relation: calls `autoSurfaceAtCompaction(...)` for `memory_context(mode="resume")`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:123:     Match: "CocoIndex bridge", "semantic neighbors", "compaction pipeline".
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:133:   - CocoIndex: warm, semantic index timestamp 2026-03-30T...
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:141:   The current code-graph plan is already scoped to JS/TS, Python, and Shell with a standardized capture vocabulary, while CocoIndex already supports 28+ languages with function-level chunking. That means the right v1 contract is:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:144:   - source-agnostic semantic retrieval from CocoIndex
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:156:   Inference from the sources: CocoIndex should do more of the cross-language conceptual bridging, while Code Graph should stay conservative and structural.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:160:   The packet's architecture decision is already explicit: PreCompact computes and caches, `SessionStart(source=compact)` injects. Splitting CocoIndex into SessionStart would reintroduce variable latency and drift at exactly the point where the packet wants deterministic post-compaction recovery. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/decision-record.md:58-74`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-045.md:170-173`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:166:   - SessionStart fallback: if cache missing, corrupt, or clearly expired, degrade to `memory_context({ mode: "resume", profile: "resume" })` plus auto-surface rather than rerunning the full 3-source merge in the foreground
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:172:   File-level dedup alone is too coarse because the same file can matter for very different reasons. A file might appear from CocoIndex because one function semantically matches the task, while the Code Graph points to a separate caller or test symbol in the same file. Because Code Graph is designed around stable node IDs and CocoIndex works at function-level chunking, the natural dedup key is the symbol when available. [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-044.md:119-123`] [SOURCE: `.opencode/specs/system-spec-kit/024-compact-code-graph/research/research.md:463-466`]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:196:   - CocoIndex: `warm` by default unless the index exposes a fresher status API later
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:264:- CocoIndex as the semantic layer
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-052.md:295:5. Make Code Graph expansion depend on both active symbols and top CocoIndex hits, not just active files.
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_14-28__upgrade-level-script.md:369:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/z_archive/007-upgrade-level-script" })` |
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_14-28__upgrade-level-script.md:381:memory_search({ specFolder: "system-spec-kit/z_archive/007-upgrade-level-script", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_14-28__upgrade-level-script.md:387:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_14-28__upgrade-level-script.md:396:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/01-01-26_18-04__generate-context-modularization.md:308:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/058-generate-context-modularization" })` |
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/01-01-26_18-04__generate-context-modularization.md:313:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/spec.md:62:`Code_Environment/Public` already operates CocoIndex, Code Graph MCP, and Spec Kit Memory. It does not yet have a Mainframe-style shared query-result cache or a self-healing loop that patches stale code-context artifacts after agent failures. Contextador appears to address both concerns, but its claims (93% token reduction, "self-improving" knowledge, cross-agent reuse) need to be verified against the actual checked-in source instead of README marketing.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/spec.md:83:- Direct comparison with current CocoIndex, Code Graph MCP, and Spec Kit Memory surfaces in this repository
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/spec.md:133:| REQ-006 | Compare Contextador against current CocoIndex, Code Graph MCP, and Spec Kit Memory surfaces | research.md cites concrete repo paths in the comparison |
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_15-53__upgrade-level-script.md:507:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/z_archive/007-upgrade-level-script" })` |
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_15-53__upgrade-level-script.md:519:memory_search({ specFolder: "system-spec-kit/z_archive/007-upgrade-level-script", limit: 10 })
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_15-53__upgrade-level-script.md:525:memory_search({ query: "orphaned", anchors: ["state"] })
.opencode/specs/system-spec-kit/z_archive/007-upgrade-level-script/scratch/legacy-memory-quarantine/15-02-26_15-53__upgrade-level-script.md:534:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/plan.md:124:- [x] Load prior context via `memory_context` and inject into strategy.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:13:| `memory_search`              | 29 | 42 | 4  | 0 | 292 | **367** | T1 Gateway | **Permanent alias** (zero-removal) |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:14:| `memory_context`             |  6 | 52 | 6  | 0 | 195 | **259** | T1 Gateway | **Permanent alias** (zero-removal) |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:17:| `memory_match_triggers`      |  2 | 34 | 12 | 0 |  61 | **109** | T2 Workflow | **2-release alias** with deprecation warning |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:35:Tier boundaries: T1 = TOTAL > 100 AND quoted in operator-facing top-doc class (`t > 0`); T2 = TOTAL 50–110 OR quoted in agent-def class (`a > 0`) without operator-facing prevalence; T3 = TOTAL < 60 AND skill-docs only (`s` exclusively populated, all other classes 0). The natural gap between T1 and T2 is between 125 and 109 (`memory_index_scan` vs `memory_match_triggers`); between T2 and T3 is between 70 and 53 (`memory_health` vs `memory_delete`). [SOURCE: bulk grep across `.opencode .claude CLAUDE.md AGENTS.md AGENTS_Barter.md AGENTS_example_fs_enterprises.md opencode.json .utcp_config.json` with 5-class file partition; 2026-04-26 iteration 2]
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:40:   - `CLAUDE.md:141, 164, 170` — `memory_match_triggers`, `memory_context`, `memory_search` (3 quotes per file × 4 files = 12 hits, matches t=12 for `memory_match_triggers`)
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:45:   This is a strong signal: the operator-facing rules layer treats only 4 tools (`memory_match_triggers`, `memory_context`, `memory_search`, `memory_save`) — plus `memory_index_scan` referenced once for post-save indexing — as first-class operator vocabulary. Per project rule "AGENTS.md updates must sync the Barter + fs-enterprises siblings" (from MEMORY.md), these 4 tools are the ones whose rename will require coordinated edits across the synced triad in a single PR. The other 17 tools can be renamed without touching the synced triad at all. [SOURCE: CLAUDE.md:141,164,170; AGENTS.md:141,164,170; AGENTS_Barter.md:181,213,219; AGENTS_example_fs_enterprises.md:160,193,199 — verified iteration 2]
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:47:4. **The agent-def class is dominated by 4 tools and shows a clean cliff at the rest.** Of 16 agent-def files (`.claude/agents/*.md` + `.opencode/agents/*.md`) that reference any memory tool, the class count distribution is: `memory_context`=52, `memory_search`=42, `memory_match_triggers`=34, `memory_list`=10, `memory_stats`=4, `memory_save`=0, all 15 others=0. The cliff between `memory_stats` (4) and the next non-zero (`memory_list`=10) is shallow but the cliff from `memory_list` (10) down to all 15 zero-counts is total. Sample quotes confirm context (e.g., `.claude/agents/deep-review.md:` `"Do NOT redundantly call memory_context or memory_match_triggers for the same information"`) — these are operator-instruction quotes, not casual mentions. `memory_save` having `a=0` is interesting: agent definitions never invoke save directly; saves are routed through `/memory:save` slash command. This means `memory_save` is a top-doc-tier quote (CLAUDE.md MEMORY SAVE RULE) but not an agent-def-tier quote. Tiering still places it as T1 because top-doc presence + skill-docs intensity (164) + handover quotes (4) carry it. [SOURCE: `.claude/agents/deep-review.md`, `.claude/agents/context.md`, plus 14 other agent files; per-file-class grep iteration 2]
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:49:5. **The 27 committed `handover.md` files quote `memory_search` 29 times — by far the most-quoted tool in operator runbooks.** Sample quotes: `.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/013-fts5-fix-and-search-dashboard/handover.md` contains `memory_search("semantic search")` returns 5 results, `memory_search` (auto), `memory_search` (deep) — these are runnable example invocations, not prose mentions, embedded in completed-spec runbooks that operators actually read during recovery. Renaming `memory_search` would invalidate these runbook examples. Combined with `memory_search`'s s=292 (skill docs) — the highest of any tool — this is the single strongest case for permanent alias retention. The next-highest handover quote is `memory_context` at 6 hits and `memory_save` at 4; everything else is ≤ 3. [SOURCE: 27× `.opencode/specs/**/handover.md` files via `find` + grep — iteration 2]
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:59:| **T1 Gateway** (>100 quotations, top-doc presence) | 4 (`memory_search`, `memory_context`, `memory_save`, `memory_index_scan`) | **Permanent alias** — never remove. Add deprecation log on call but always succeed. | These tools have 367/259/172/125 file-level quotes including operator runbooks (handover.md), top-level rules (CLAUDE.md sync triad), and 16 agent definitions. Permanent retention is the only way to preserve external quotability. |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:60:| **T2 Workflow** (50–110 quotations, agent-def presence) | 4 (`memory_match_triggers`, `memory_stats`, `memory_list`, `memory_health`) | **2-release alias window** — emit deprecation warnings starting release N+1, remove in release N+3. | Tools quoted in agent definitions and CLAUDE.md gate prose; `memory_match_triggers` has 12 top-doc hits across the triad (Gate 1 protocol). 2-release window allows agent-def updates and external integration migration. |
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:79:- Bulk grep `grep -rE '\bmemory_(...21 names...)\b' --include='*.md' --include='*.json' .opencode .claude CLAUDE.md AGENTS.md AGENTS_Barter.md AGENTS_example_fs_enterprises.md opencode.json .utcp_config.json` — produced raw token-level density (top: memory_search=21314, memory_context=18136, memory_save=10184)
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:87:- Skill-level SKILL.md per-tool counts (memory_context=8, memory_search=12, memory_save=5, memory_match_triggers=2, memory_index_scan=10) — confirms intensity tracks tier ranking
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/000-release-cleanup/001-memory-terminology/research/iterations/iteration-002.md:100:- **What did not work and why**: The first bulk grep returned token-level counts that misleadingly inflated `memory_search` to 21314 because the regex matched multiple times per line and matched file paths containing `memory_`. The correct signal was per-file `wc -l` of `grep -l` output, not raw `grep` count. Lesson: always partition by file class with `wc -l` for "external quotation density" questions; raw `grep -c` mixes path matches and multi-match lines.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/scratch/phase-research-prompt.md:33:`Code_Environment/Public` already has CocoIndex for semantic code search, Code Graph MCP for structural queries, Spec Kit Memory for context preservation, and `validate.sh` for spec validation. It does not currently have Codesight-style automated `CLAUDE.md` / `.cursorrules` / `codex.md` / `AGENTS.md` generation from a single project scan, per-AI-tool profile generation, or a blast-radius command built around reverse dependency traversal. Do not describe this repo as lacking semantic search or structural analysis; compare Codesight against the current stack, not a stale baseline.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/scratch/phase-research-prompt.md:49:13. Use CocoIndex first for concept-based tracing and grep second for exact follow-up checks. When tracing detector implementations, prefer semantic discovery of the relevant subsystem before line-level confirmation.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/scratch/phase-research-prompt.md:88:- Do compare Codesight against current `Code_Environment/Public` capabilities so recommendations target real gaps instead of reinventing CocoIndex, Code Graph MCP, or Spec Kit Memory.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/scratch/phase-research-prompt.md:145:Rank findings in this order: high-impact/low-effort profile-generation patterns to adopt now, high-impact/medium-effort blast-radius and hot-file ideas to prototype later, and clearly out-of-scope or low-signal items such as HTML dashboard polish to reject. Prefer recommendations that complement CocoIndex, Code Graph MCP, and Spec Kit Memory rather than duplicating them.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:10:5. Design instruction-file auto-trigger patterns that force `memory_context()` and `code_graph_scan()`/`code_graph_context()` behavior.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:30:- research/exploration -> `memory_match_triggers()` + `memory_context()`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:31:- resume prior work -> `memory_context(... mode: "resume", profile: "resume" ...)`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:39:[SOURCE: GEMINI.md search on 2026-03-31 found `memory_context` instructions but no Gemini-specific `SessionStart`, `PreCompress`, or `code_graph_scan` protocol]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:114:I also checked the upstream `google-gemini/gemini-cli` repo and code search for `.mcp.json` returned **0 results**, which strongly suggests `.mcp.json` is **not** an official Gemini-native config surface.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:128:[SOURCE: GitHub code search `repo:google-gemini/gemini-cli ".mcp.json"` returned 0 results on 2026-03-31]
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:137:| **Resume / continuation** | `resume`, `continue`, `previous work`, `after clear`, spec-folder continuation | `memory_match_triggers(prompt)` -> `memory_context({ input: prompt, mode: "resume", profile: "resume" })` |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:138:| **General exploration** | broad understanding / research requests | `memory_match_triggers(prompt)` -> `memory_context({ input: prompt, mode: "auto" })` |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:140:| **Semantic implementation questions** | `how is X implemented`, `find code that`, `similar code` | `cocoindex_code.search(...)` first, then graph expansion only if structure matters |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:150:1. Call `memory_match_triggers(prompt)`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:151:2. Call `memory_context({ input: prompt, mode: "auto" })`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:153:   `memory_context({ input: prompt, mode: "resume", profile: "resume" })`.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:158:5. For semantic "how is X implemented?" questions, call `cocoindex_code.search(...)`
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:212:  - no guaranteed first-turn `memory_context()` execution
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-087.md:256:- GitHub code search against `google-gemini/gemini-cli` for `.mcp.json`, `context.fileName`, and hook events
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/01-01-26_17-45__generate-context-modularization-spec.md:259:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/058-generate-context-modularization" })` |
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/01-01-26_17-45__generate-context-modularization-spec.md:264:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-042.md:16:   `CodeBERT`: still a credible self-hosted baseline for code search and a useful reranker/fine-tuning starting point, but it is an older academic model rather than the frontier production choice.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:14:CODEX.md exists at the repo root and contains: (a) compaction recovery instructions telling the AI to call `memory_context({ mode: "resume" })`, (b) query-intent routing section mapping semantic/structural/continuity queries to tools, (c) available MCP tools list including Code Graph tools (`code_graph_scan`, `code_graph_query`, `code_graph_status`, `code_graph_context`). However, there is NO instruction to auto-trigger code graph context at session start or on first tool call. The code graph tools are listed but not connected to any automatic workflow.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:24:The `.agents/settings.json` specifies `"context": { "fileName": ["GEMINI.md", "AGENTS.md"] }` -- these are the instruction files loaded at session start. Both AGENTS.md and GEMINI.md are identical to the root CLAUDE.md (the universal AI Assistant Framework). There is NO Copilot-specific instruction file (no COPILOT.md exists). This means Copilot CLI gets the full universal framework including Gate 1 (`memory_match_triggers`), Gate 2 (skill routing), and Gate 3 (spec folder) -- but like Codex CLI, has NO code graph auto-trigger instructions.
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:43:1. `memory_match_triggers(prompt)` -- surface constitutional + triggered context
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:44:2. `memory_context({ input: "[user's first message]", mode: "auto" })` -- intent-aware retrieval
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:51:1. **CONTEXT LOAD** → On first turn: call `memory_match_triggers(prompt)`, then if file paths detected in request, call `code_graph_context({ seeds: [{ provider: "manual", filePath: "<path>" }], queryMode: "neighborhood" })` for structural context
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:58:**Proposed approach**: Since Copilot CLI loads AGENTS.md (which IS the universal CLAUDE.md framework), the instruction already exists at Gate 1 (`memory_match_triggers`). The GAP is code graph. Add a new subsection to the universal CLAUDE.md "Quick Reference: Common Workflows" table:
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:60:| **Session start**     | `memory_match_triggers(prompt)` → `code_graph_status()` → if stale: `code_graph_scan()` → proceed |
.opencode/specs/system-spec-kit/024-compact-code-graph/research/iterations/iteration-074.md:103:This is iteration 74 of 75 (penultimate). The recommended next focus for the final iteration is: **Cross-runtime UX parity summary table and final consolidation** -- produce a definitive comparison matrix showing what each runtime gets automatically (hooks vs instructions vs manual) for memory context, code graph context, CocoIndex, and session lifecycle. This serves as the capstone finding for the entire Segment 6 research.
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/02-01-26_12-50__generate-context-modularization.md:310:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/058-generate-context-modularization" })` |
.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/058-generate-context-modularization/scratch/legacy-memory-quarantine/02-01-26_12-50__generate-context-modularization.md:315:2. **Load memory context** - Use memory_search to surface prior work
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/scratch/phase-research-prompt.md:37:`Code_Environment/Public` already has CocoIndex for semantic code search, Code Graph MCP for structural queries, and Spec Kit Memory for semantic memory retrieval and saved session context. What it does not currently have is a Mainframe-style shared query-result cache across machines or a self-healing code-context feedback loop that patches stale context artifacts after agent failure reports.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/scratch/phase-research-prompt.md:79:12. Compared with CocoIndex, Code Graph MCP, and Spec Kit Memory, what is genuinely new in Contextador's query model, and what would only duplicate behavior this repo already has?
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/scratch/phase-research-prompt.md:87:- Do compare Contextador's query patterns against this repo's existing CocoIndex, Code Graph, and Spec Kit Memory surfaces.
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/scratch/phase-research-prompt.md:154:- explicit comparison against CocoIndex, Code Graph MCP, and Spec Kit Memory
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/002-codesight/graph-metadata.json:213:    "causal_summary": "Phase 2 of `001-research-graph-context-systems` is a read-only audit of the codesight external Node.js/TypeScript skill (zero-runtime-dependency CLI that scans a project root and generates AI-assistant context artifac7166:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1584:      error: 'memory_context failed due to an internal error',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147167:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1606:const handle_memory_context = handleMemoryContext;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147168:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1609:  handle_memory_context,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147169:.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:4:// Dispatch for L1 Orchestration tool: memory_context (T303).
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147170:.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:11:export const TOOL_NAMES = new Set(['memory_context']);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147171:.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:16:    case 'memory_context': return handleMemoryContext(parseArgs<ContextArgs>(validateToolArgs('memory_context', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147174:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:426:- `memory_context` (unified context retrieval)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147175:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:427:- `memory_search` (semantic search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147176:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:428:- `memory_match_triggers` (fast trigger matching)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147179:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:465:- [ ] `memory_search()` returns results (or empty if no memories are indexed yet)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147180:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:530:### memory_context: Unified Context Retrieval
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147181:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:532:`memory_context()` is the primary entry point for context loading. It detects task intent and routes to the optimal retrieval strategy automatically.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147183:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:548:### memory_search: Semantic Search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147184:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:550:`memory_search()` runs vector-based similarity search across all indexed memories.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147185:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:559:### memory_match_triggers: Fast Keyword Lookup
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147186:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:561:`memory_match_triggers()` provides sub-50ms keyword-based matching. Use it for immediate context surfacing at the start of a conversation.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147188:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:629:- `ContextEnvelope`: Wraps all `memory_context()` responses with metadata (mode used, memories returned, intent detected)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147189:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:681:**Behind the scenes:** The AI calls `memory_context()` with `mode: "resume"` and `anchors: ["state", "next-steps"]`, then returns the previous session state.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147190:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:692:1. AI calls `memory_context({ input: "add user profiles", mode: "auto" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147192:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1047:MCP TOOLS: memory_context, memory_search, memory_match_triggers,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147193:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1064:| v1.7.x | 2026-02-20 | Cross-encoder reranking enabled by default. Co-activation score boost fix. Query expansion on deep mode. Evidence gap warnings. MMR reranking with intent-mapped lambda. Phase system support (recursive validation, phase detection scoring). Feature flag updates. `memory_context` tokenUsage parameter. 28-tool surface area. |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147204:.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1263:      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147205:.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1264:      : 'memory_search({ query: "last session" })';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147207:.opencode/skills/system-spec-kit/mcp_server/README.md:9:  - "memory_context"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147208:.opencode/skills/system-spec-kit/mcp_server/README.md:10:  - "memory_search"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147212:.opencode/skills/system-spec-kit/mcp_server/README.md:200:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147214:.opencode/skills/system-spec-kit/mcp_server/README.md:547:**Query routing:** Structural queries (callers, imports, dependencies) go to `code_graph_query`. Semantic and concept queries go to CocoIndex (`mcp__cocoindex_code__search`). Session and memory queries go to `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147215:.opencode/skills/system-spec-kit/mcp_server/README.md:557:**Start here for most tasks**: `memory_context` (L1) automatically figures out what you need. Use the lower-level tools when you want precise control.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147216:.opencode/skills/system-spec-kit/mcp_server/README.md:563:##### `memory_context`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147218:.opencode/skills/system-spec-kit/mcp_server/README.md:587:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147220:.opencode/skills/system-spec-kit/mcp_server/README.md:601:Resume session with combined memory, code graph and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. The response carries freshness-aware code-graph status (`fresh`, `stale`, `empty`, `error`) instead of count-only health. For the canonical first-call recovery path on session start or after `/clear`, prefer `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147224:.opencode/skills/system-spec-kit/mcp_server/README.md:622:##### `memory_search`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147225:.opencode/skills/system-spec-kit/mcp_server/README.md:646:  "tool": "memory_search",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147226:.opencode/skills/system-spec-kit/mcp_server/README.md:674:##### `memory_match_triggers`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147227:.opencode/skills/system-spec-kit/mcp_server/README.md:688:  "tool": "memory_match_triggers",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147228:.opencode/skills/system-spec-kit/mcp_server/README.md:1326:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147232:.opencode/skills/system-spec-kit/mcp_server/README.md:1538:| Find a past decision | `memory_context` | Set `intent: "find_decision"` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147233:.opencode/skills/system-spec-kit/mcp_server/README.md:1539:| Search for specific terms | `memory_search` | Use `concepts: ["term1", "term2"]` for AND search |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147234:.opencode/skills/system-spec-kit/mcp_server/README.md:1540:| Check triggers on every prompt | `memory_match_triggers` | Pass the user's prompt text |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147235:.opencode/skills/system-spec-kit/mcp_server/README.md:1556:**What you see**: Irrelevant or low-scoring results from `memory_search` or `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147236:.opencode/skills/system-spec-kit/mcp_server/README.md:1567:{ "tool": "memory_search", "arguments": { "query": "your query", "min_quality_score": 0.5 } }
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147237:.opencode/skills/system-spec-kit/mcp_server/README.md:1717:Start with `memory_context` for all retrieval tasks. It handles intent detection and routing automatically. Use `memory_search` when you want explicit control over channels. Use `memory_match_triggers` when processing a raw prompt at the start of each turn. Use L4-L7 tools only for mutation, analysis or maintenance.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147238:.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:416:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147239:.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:709:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147242:.opencode/skills/system-spec-kit/mcp_server/lib/session/README.md:93:1. User queries memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147245:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:42:  name: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147246:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:43:  description: '[L1:Orchestration] Unified entry point for context retrieval with intent-aware routing. START HERE for most memory operations. For session recovery, use mode: \'resume\' with profile: \'resume\'. Automatically detects task intent (add_feature, fix_bug, refactor, security_audit, understand, find_spec, find_decision) and routes to optimal retrieval strategy. Modes: auto (default), quick (trigger-based), deep (comprehensive), focused (intent-optimized), resume (session recovery). Token Budget: 3500. For code search by concept/intent, prefer mcp__cocoindex_code__search (CocoIndex). For structural code queries (callers, imports), prefer code_graph_query.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147247:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:44:  inputSchema: { type: 'object', additionalProperties: false, properties: { input: { type: 'string', minLength: 1, description: 'The query, prompt, or context description (required)' }, mode: { type: 'string', enum: ['auto', 'quick', 'deep', 'focused', 'resume'], default: 'auto', description: 'Context retrieval mode: auto (detect intent), quick (fast triggers), deep (comprehensive search), focused (intent-optimized), resume (session recovery)' }, intent: { type: 'string', enum: ['add_feature', 'fix_bug', 'refactor', 'security_audit', 'understand', 'find_spec', 'find_decision'], description: 'Explicit task intent. If not provided and mode=auto, intent is auto-detected from input.' }, specFolder: { type: 'string', description: 'Limit context to specific spec folder' }, tenantId: { type: 'string', description: 'Tenant boundary for governed retrieval when memory_context routes to memory_search.' }, userId: { type: 'string', description: 'User boundary for governed retrieval when memory_context routes to memory_search.' }, agentId: { type: 'string', description: 'Agent boundary for governed retrieval when memory_context routes to memory_search.' }, sharedSpaceId: { type: 'string', description: 'Shared-space boundary for governed retrieval when memory_context routes to memory_search.' }, limit: { type: 'number', minimum: 1, maximum: 100, description: 'Maximum results (mode-specific defaults apply)' }, sessionId: { type: 'string', description: 'Optional server-issued session identifier for working-memory continuity. When provided, it must match an existing server-managed session or the call is rejected. Omit it to let the server generate a new session for this request.' }, enableDedup: { type: 'boolean', default: true, description: 'Enable session deduplication' }, includeContent: { type: 'boolean', default: false, description: 'Include full file content in results' }, includeTrace: { type: 'boolean', default: false, description: 'Include provenance-rich trace data (scores, source, trace) in results when underlying memory_search is called' }, tokenUsage: { type: 'number', minimum: 0.0, maximum: 1.0, description: "Optional caller token usage ratio (0.0-1.0)" }, anchors: { type: 'array', items: { type: 'string' }, description: 'Filter content to specific anchors (e.g., ["state", "next-steps"] for resume mode)' }, profile: { type: 'string', enum: ['quick', 'research', 'resume', 'debug'], description: 'Optional response profile formatter. Returns a reduced or mode-aware response shape when profile formatting is enabled.' } }, required: ['input'] },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147248:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:49:  name: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147251:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:190:// E3: Simplified search — 3 params, sensible defaults, delegates to memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147252:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:193:  description: '[L2:Core] Simplified search — query + optional limit + optional spec folder. Delegates to memory_search with sensible defaults (intent auto-detect ON, dedup ON, content included, limit 10). Use this when you want fast search without configuring 31 parameters.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147253:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:211:  name: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147256:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:741:  description: '[L1:Orchestration] Resume session with combined memory, code graph, and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. For the canonical first-call recovery path on session start or after /clear, prefer session_bootstrap. Use minimal: true to skip the heavy memory context call and return code graph, CocoIndex, structural context, hints, and session-quality metadata without the full memory payload.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147264:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:86:  'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147265:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:87:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147266:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:89:  'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147275:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:460:    recommendedCalls.push('memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147276:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:463:    recommendedCalls.push('memory_match_triggers({ prompt: "<your task>" })');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147277:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:482:      graphRetrieval: 'For broad topic questions, use memory_search with retrievalLevel: "global" for community-level results. For specific memories, use "local" (default). Use "auto" for automatic fallback.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147278:.opencode/skills/system-spec-kit/mcp_server/tools/README.md:27:- `context-tools.ts` - dispatch for `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147279:.opencode/skills/system-spec-kit/mcp_server/tools/README.md:40:- `memory-tools.ts` implements the `memory_quick_search` delegation path by building a richer `memory_search` request and relabeling the returned envelope metadata back to `memory_quick_search`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147283:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:112:  includeTrace: z.boolean().optional(), // CHK-040: Forward to internal memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147286:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:397:  memory_context: memoryContextSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147287:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:398:  memory_search: memorySearchSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147288:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:400:  memory_match_triggers: memoryMatchTriggersSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147291:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:462:  memory_context: ['input', 'mode', 'intent', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'sessionId', 'enableDedup', 'includeContent', 'includeTrace', 'tokenUsage', 'anchors', 'profile'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147292:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:463:  memory_search: ['cursor', 'query', 'concepts', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'sessionId', 'enableDedup', 'tier', 'contextType', 'useDecay', 'includeContiguity', 'includeConstitutional', 'enableSessionBoost', 'enableCausalBoost', 'includeContent', 'anchors', 'min_quality_score', 'minQualityScore', 'bypassCache', 'rerank', 'applyLengthPenalty', 'applyStateLimits', 'minState', 'intent', 'autoDetectIntent', 'trackAccess', 'includeArchived', 'mode', 'includeTrace', 'profile'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147293:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:465:  memory_match_triggers: ['prompt', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'session_id', 'turnNumber', 'include_cognitive'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147296:.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts:90: * reliable retrieval via the `memory_match_triggers` tool. The scoring
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147297:.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts:224:  //   recovery (0.20)      — A memory_context({ mode: "resume" }) call is the most
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147298:.opencode/skills/system-spec-kit/mcp_server/hooks/README.md:70:- `MEMORY_AWARE_TOOLS` currently includes `memory_context`, `memory_search`, `memory_match_triggers`, `memory_list`, `memory_save`, and `memory_index_scan`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147299:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:62:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147300:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:64:  'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147301:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:78:    case 'memory_search':         return handleMemorySearch(parseArgs<SearchArgs>(validateToolArgs('memory_search', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147302:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:80:      // E3: Delegate to memory_search with sensible defaults
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147303:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:99:    case 'memory_match_triggers': return handleMemoryMatchTriggers(parseArgs<TriggerArgs>(validateToolArgs('memory_match_triggers', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147306:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:50:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147307:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:61:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147308:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:77:      content: 'Context was compacted and auto-recovered from the cached compact brief. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147311:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:140:        '- `memory_context({ input, mode })` — unified context retrieval',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147312:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:141:        '- `memory_match_triggers({ prompt })` — fast trigger matching',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147313:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:142:        '- `memory_search({ query })` — semantic search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147315:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:185:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147316:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:190:      content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147317:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:202:      content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147320:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:51:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147321:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:62:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147322:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:73:      content: 'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147323:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:106:        '- `memory_context({ input, mode })` - unified context retrieval',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147324:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:107:        '- `memory_match_triggers({ prompt })` - fast trigger matching',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147325:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:108:        '- `memory_search({ query })` - semantic search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147327:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:149:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147328:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:155:    content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147329:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:163:    content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147335:.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:175:Packet `026-graph-and-context-optimization/010-fts-capability-cascade-floor` freezes the lexical capability contract that packet `002-implement-cache-warning-hooks` now consumes. `memory_search` responses expose:
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147339:.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:384:  it('C13: Response meta.tool is memory_search', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147340:.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:388:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147343:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/README.md:31:Hooks are transport reliability, not separate business logic. They call the same retrieval primitives (`memory_match_triggers`, `memory_context`) that other runtimes call explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147344:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/compact-inject.ts:63:    'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147352:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:59:    it('T516-2: handle_memory_search alias is exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147353:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:60:      expect(typeof handler.handle_memory_search).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147354:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:83:      validateToolInputSchema('memory_context', {}, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147355:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:119:      validateToolInputSchema('memory_context', { input: 'resume', mode: 'invalid-mode' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147356:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:133:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147357:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:137:    expect(errorSpy.mock.calls.some((call) => String(call[0]).includes('[schema-validation] memory_search:'))).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147358:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:240:   4. memory_search LIMIT CONTRACT (schema + runtime alignment)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147359:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:243:describe('memory_search limit contract', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147360:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:246:      validateToolInputSchema('memory_search', { cursor: 'opaque-cursor-token' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147361:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:252:      validateToolArgs('memory_search', { cursor: 'opaque-cursor-token' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147362:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:258:      validateToolInputSchema('memory_search', { concepts: ['alpha', 'beta'] }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147363:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:264:      validateToolInputSchema('memory_search', {}, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147364:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:270:      validateToolArgs('memory_search', { query: 'ab', limit: 100 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147365:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:276:      validateToolArgs('memory_search', { query: 'ab', limit: 101 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147366:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:282:      validateToolInputSchema('memory_search', { query: 'ab', limit: 101 }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147367:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:288:      validateToolArgs('memory_search', { concepts: ['solo'] });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147368:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:292:  it('public schema rejects unknown memory_search parameters', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147369:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:294:      validateToolInputSchema('memory_search', { query: 'valid query', unexpected: true }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147370:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:300:      validateToolInputSchema('memory_search', { query: 'a' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147371:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:304:  it('runtime rejects unknown memory_search parameters', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147372:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:306:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147373:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:310:  it('runtime accepts governed scope fields for memory_search', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147374:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:312:      validateToolArgs('memory_search', {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147375:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:322:  it('public and runtime schemas accept response profiles for memory_search', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147376:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:329:      validateToolInputSchema('memory_search', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147377:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:331:    expect(validateToolArgs('memory_search', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147378:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:336:  it('public and runtime schemas accept governed scope fields for memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147380:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:346:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147381:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:348:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147382:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:351:  it('public and runtime schemas accept response profiles for memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147385:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:358:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147386:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:360:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147387:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:378:  it('public and runtime schemas accept governed scope fields for memory_match_triggers', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147389:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:389:      validateToolInputSchema('memory_match_triggers', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147390:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:391:    expect(validateToolArgs('memory_match_triggers', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147391:.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:977:  // Including it here caused all candidates to be filtered out when memory_context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147396:.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:52: * Token-pressure policy for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147397:.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:60: * Automatic session resume context injection for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147406:.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34:The `pipeline/` directory implements the core retrieval pipeline behind `memory_search`. Each search request flows through four sequential stages, each with a defined I/O contract and clear responsibility boundary. The pipeline supports hybrid, vector and multi-concept search types with optional deep-mode query expansion, cross-encoder reranking, MMR diversity pruning and MPAB chunk-to-parent reassembly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147415:.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:482:describe('T059: autoDetectIntent Parameter (memory_search)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147416:.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:4:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147437:.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:42:    toolPattern: /^(read|memory_context|memory_search|memory_list)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147438:.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:49:    toolPattern: /^(grep|memory_search)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147439:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:76:    it('T517-2: handle_memory_match_triggers alias exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147440:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:77:      expect(typeof handler.handle_memory_match_triggers).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147448:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:6:  { tool: 'memory_context', handler: 'handleMemoryContext', layer: 'L1' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147449:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:7:  { tool: 'memory_search', handler: 'handleMemorySearch', layer: 'L2' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147450:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:8:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers', layer: 'L2' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147451:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:33:  { camel: 'handleMemorySearch', snake: 'handle_memory_search' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147452:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:34:  { camel: 'handleMemoryMatchTriggers', snake: 'handle_memory_match_triggers' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147453:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:56:  { camel: 'handleMemoryContext', snake: 'handle_memory_context' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147454:.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:23:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147457:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:82:      const key1 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147458:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:83:      const key2 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147459:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:88:      const key1 = generateCacheKey('memory_search', { query: 'auth' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147460:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:89:      const key2 = generateCacheKey('memory_search', { query: 'login' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147461:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:95:      const key1 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147462:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:352:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147463:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:353:      const key2 = generateCacheKey('memory_search', { query: 'test2' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147464:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:355:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147465:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:356:      set(key2, 'value2', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147466:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:358:      const invalidated = invalidateByTool('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147467:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:366:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147468:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:369:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147469:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:380:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147470:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:383:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147471:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:394:      const searchKey = generateCacheKey('memory_search', { query: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147472:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:395:      const triggerKey = generateCacheKey('memory_match_triggers', { prompt: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147473:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:396:      set(searchKey, 'search_result', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147474:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:397:      set(triggerKey, 'trigger_result', { toolName: 'memory_match_triggers' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147475:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:423:      const key = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147476:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:427:        'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147477:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:436:      expect(invalidateByTool('memory_search')).toBe(0);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147478:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:439:      const second = withCache('memory_search', args, async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147479:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:589:      const key = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147480:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:593:        'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147481:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:603:      const second = withCache('memory_search', args, async () => 'fresh-after-shutdown');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147482:.opencode/skills/system-spec-kit/mcp_server/lib/enrichment/passive-enrichment.ts:129:      return ['[session] Context quality is CRITICAL. Consider running `memory_context({ mode: "resume" })` or `session_health` to diagnose.'];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147484:.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:4:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147486:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:181:const key = generateCacheKey('memory_search', { query: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147487:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:184:set(key, searchResults, { toolName: 'memory_search', ttlMs: 30000 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147488:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:196:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147489:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:210:// Automatically clears memory_search, memory_match_triggers, etc.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147490:.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:312:    'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147491:.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:313:    'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147492:.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:314:    'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147504:.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:223:    followUps.push(`Use memory_context with specFolder "${uniqueFolders[0]}" for full context`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147510:.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:53:  memory_search: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147511:.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:55:  memory_context: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147512:.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:56:  memory_match_triggers: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147515:.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:39:| Tool-Specific Hints | 6 tools | memory_search, checkpoint_restore, memory_save, memory_index_scan, memory_drift_why, memory_causal_link |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147516:.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:132:  return buildErrorResponse('memory_search', error, { query });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147517:.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:142:const hint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147520:.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:250:  it('T020-02: Generates memory_search command with sessionId when specFolder is not provided', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147521:.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:254:  it('T020-03: Generates generic memory_search when neither specFolder nor sessionId is provided', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147529:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:50:    tools: ['memory_context', 'session_resume', 'session_bootstrap']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147530:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:59:    tools: ['memory_search', 'memory_quick_search', 'memory_save', 'memory_match_triggers']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147531:.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:133:    expect(matchRule('memory_search', 'spec.md error context')).not.toBeNull();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147532:.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:134:    expect(matchRule('memory_context', 'spec.md metadata')).not.toBeNull();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147533:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:357:      'Use memory_match_triggers() for prompt-based matching instead'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147534:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:360:    toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147536:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:539:      'Check memory_search() for existing similar content'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147537:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:694:  memory_search: {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147538:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:700:        'Try memory_match_triggers() for trigger-based matching'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147539:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:703:      toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147541:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:30:      "expectedResultDescription": "Should surface memories about adaptive-fusion.ts (7 intent profiles), intent-classifier.ts, and memory_context intent routing. Cross-document because the behavior spans multiple modules.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147543:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:85:      "query": "memory_context returns wrong results when token pressure is high",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147547:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:251:      "notes": "From T007b Pattern 3: feature description passed to memory_context before implementation."
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147548:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:415:      "query": "the memory_search tool returns stale results after index rebuild",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147549:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:425:      "query": "what is the difference between memory_context and memory_search for context retrieval",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147550:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:430:      "expectedResultDescription": "Should surface both memory_context (L1 unified entry) and memory_search (L2 core) tool schemas and any documentation comparing their use cases.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147554:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:725:      "query": "when should I use memory_search versus memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147555:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:132:const budget = getTokenBudget('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147556:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:139:const enhanced = enhanceDescription('memory_search', 'Search memories');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147564:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:48:  liveBaselineResolution: 'code_graph_query' | 'memory_context' | 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147565:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:143:    return 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147566:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:146:  return 'memory_context';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147567:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:162:    if (resolution === 'memory_context_then_grep') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147570:.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:89:describe('memory_context advisory metadata', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147587:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:181:  it('T022: memory_search has tool-specific hints', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147588:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:182:    expect(TOOL_SPECIFIC_HINTS.memory_search).toBeDefined();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147589:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:183:    expect(typeof TOOL_SPECIFIC_HINTS.memory_search).toBe('object');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147590:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:221:  it('T029: memory_search EMBEDDING_FAILED has contextual hint', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147591:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:224:      TOOL_SPECIFIC_HINTS.memory_search?.[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147592:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:244:    const searchHint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147593:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:246:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147594:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:301:      'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147595:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:315:    const hasSearch = hasSpecificHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147596:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:356:    const searchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147597:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:362:    const searchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147598:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:365:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147599:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:669:  it('T087: QUERY_TOO_LONG suggests memory_match_triggers()', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147600:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:672:      a.includes('memory_match_triggers()')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147602:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:713:    const toolSpecific = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147603:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:718:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147604:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:725:    const allSearchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147608:.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:8:// Phase 020: Integrated into memory_context handler for query-intent
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147634:.opencode/skills/system-spec-kit/mcp_server/tests/memory-tools.vitest.ts:12:    content: [{ type: 'text', text: JSON.stringify({ data: { results: [], count: 0 }, meta: { tool: 'memory_search' } }) }],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147636:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:1:// TEST: memory_context per-channel eval logging (T056)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147637:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:88:describe('T056: memory_context emits per-strategy channel eval rows', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147639:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:159:      'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147640:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:160:      'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147641:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:162:      'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147644:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:292:      'memory_context', 'memory_search', 'memory_quick_search', 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147647:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:927:        { id: 'call-1', params: { name: 'memory_search', arguments: {} } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147648:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:944:      expect(callArgs[0]).toBe('memory_search')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147649:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1054:              name: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147650:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1103:        memoryAwareTools: new Set<string>(['memory_search']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147651:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1113:        { id: 'call-5', params: { name: 'memory_search', arguments: { query: 'hook validation' } } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147652:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1123:    it('T000g: memory_context resume mode invokes TM-05 compaction hook at runtime', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147653:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1131:        memoryAwareTools: new Set<string>(['memory_context']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147655:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1144:          params: { name: 'memory_context', arguments: { input: 'session resume context', mode: 'resume' } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147657:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1157:    it('T000h: memory_context non-resume mode keeps SK-004 memory-aware path', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147658:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1164:        memoryAwareTools: new Set<string>(['memory_context']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147659:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1177:          params: { name: 'memory_context', arguments: { input: 'focused retrieval context', mode: 'focused' } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147660:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1563:      const response = errorsModule!.buildErrorResponse!('memory_search', testError, { query: 'test' })
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147661:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1581:      const hint = errorsModule!.getRecoveryHint!('memory_search', 'UNKNOWN_TOOL')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147662:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1614:    it('T28: L1 budget = 3500 (memory_context)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147663:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1619:      expect(layerDefs!.getTokenBudget!('memory_context')).toBe(3500)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147664:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1622:    it('T28b: L2 budget = 3500 (memory_search)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147665:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1627:      expect(layerDefs!.getTokenBudget!('memory_search')).toBe(3500)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147666:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1703:    const expectedAwareTools = ['memory_context', 'memory_search', 'memory_match_triggers', 'memory_list', 'memory_save', 'memory_index_scan']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147667:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2084:      'memory_context': '[L1:Orchestration]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147668:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2085:      'memory_search': '[L2:Core]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147669:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2086:      'memory_match_triggers': '[L2:Core]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147670:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2131:    it('T000e: memory_context supports optional tokenUsage (0.0-1.0)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147671:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2132:      expect(toolSchemasCode).toMatch(/name:\s*'memory_context'[\s\S]*?tokenUsage:\s*\{\s*type:\s*'number'/)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147672:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2315:        'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147673:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2341:      expect(result).toContain('memory_context')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147674:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2342:      expect(result).toContain('memory_search')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147676:.opencode/skills/system-spec-kit/mcp_server/tests/tiered-injection-turnNumber.vitest.ts:183:      expect(typeof handlerExports.handle_memory_match_triggers).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147677:.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:1:// TEST: memory_search per-channel eval logging (T056)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147678:.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:106:describe('T056: memory_search emits per-channel eval rows', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147680:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:30:    tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147681:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:37:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147682:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:43:    tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147683:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:176:  { tool: 'memory_context', handler: 'handleMemoryContext' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147684:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:177:  { tool: 'memory_search', handler: 'handleMemorySearch' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147685:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:179:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147699:.opencode/skills/system-spec-kit/mcp_server/tests/review-fixes.vitest.ts:41:    const result = validateToolArgs('memory_search', {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147703:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:127:  it('returns null for memory_context (prevents recursive surfacing)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147704:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:128:    const result = await autoSurfaceAtToolDispatch('memory_context', { input: 'some context' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147705:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:132:  it('returns null for memory_search', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147706:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:133:    const result = await autoSurfaceAtToolDispatch('memory_search', { query: 'some query' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147707:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:137:  it('returns null for memory_match_triggers', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147708:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:138:    const result = await autoSurfaceAtToolDispatch('memory_match_triggers', { prompt: 'some prompt' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147723:.opencode/skills/system-spec-kit/mcp_server/tests/session-manager-extended.vitest.ts:626:      expect(md).toContain('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147724:.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:18:        memory_context: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147725:.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:19:        memory_search: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147726:.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:21:        memory_match_triggers: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147734:.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:304:  `).run(1, 'sess-1', 1, 0.9, now, later, 2, 1, 1, 'memory_search', 'call-1', 'rule-1', 0);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147735:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:117:        memory_context: 'L1',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147736:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:118:        memory_search: 'L2',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147737:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:120:        memory_match_triggers: 'L2',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147738:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:194:        { tool: 'memory_context', expected: '[L1:Orchestration]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147739:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:195:        { tool: 'memory_search', expected: '[L2:Core]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147740:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:221:      const result = mod.enhanceDescription('memory_context', 'Some description text');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147741:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:227:        { tool: 'memory_search', desc: 'Search memories', prefix: '[L2:Core]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147742:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:242:      expect(mod.enhanceDescription('memory_context', '')).toBe('[L1:Orchestration] ');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147743:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:252:        { tool: 'memory_context', expected: 3500 },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147744:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:253:        { tool: 'memory_search', expected: 3500 },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147745:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:270:      expect(typeof mod.getTokenBudget('memory_context')).toBe('number');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147746:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:280:      const info = expectLayerInfo(mod.getLayerInfo('memory_context'));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147747:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:287:      expect(info.tools).toContain('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147748:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:291:      const info1 = mod.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147749:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:292:      const info2 = mod.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147750:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:301:      const info = expectLayerInfo(mod.getLayerInfo('memory_search'));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147751:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:430:      const toolSamples = ['memory_context', 'memory_search', 'memory_list',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147780:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:20:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147781:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:58:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147782:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:97:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147783:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:108:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147784:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:135:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147785:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:143:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147786:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:152:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147787:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:186:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147788:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:206:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147789:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:254:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147790:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:312:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147791:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:352:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147792:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:363:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147793:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:373:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147794:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:384:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147795:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:409:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147796:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:287:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147797:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:296:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147798:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:302:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147799:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:310:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147800:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:311:    expect(resp.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147801:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:318:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147802:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:328:  it('F7: Tool-specific hints included for memory_search + E001', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147803:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:330:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147804:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:353:    const err = createErrorWithHint('E040', 'fail', {}, 'memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147805:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:469:  it('K2: Has memory_search, checkpoint_restore, memory_save', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147806:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:470:    expect('memory_search' in TOOL_SPECIFIC_HINTS).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147807:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:476:    const searchHints = TOOL_SPECIFIC_HINTS['memory_search'];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147808:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:492:  it('L1: Returns tool-specific hint for memory_search + E001', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147809:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:493:    const hint = getRecoveryHint('memory_search', 'E001');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147810:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:512:    const hint = getRecoveryHint('memory_search', 'E040');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147811:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:524:  it('M1: Returns true for known tool+code (memory_search, E001)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147812:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:525:    expect(hasSpecificHint('memory_search', 'E001')).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147813:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:543:    const hints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147814:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:550:    const hints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147826:.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:50:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147827:.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:68:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147828:.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:83:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147885:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:86:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147906:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:32:  handle_memory_context,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147914:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:238:   T021-T030: handle_memory_context MAIN HANDLER TESTS
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147915:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:242:  it('T021: handle_memory_context is a function', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147916:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:289:  it('T029: handleMemoryContext is alias for handle_memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147917:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:290:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147951:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:847:  it('T101: handle_memory_context is exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147953:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:868:  it('T105: handleMemoryContext is same as handle_memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147954:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:869:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147955:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:902:      meta: { tool: 'memory_search' }
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:147958:.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:123:describe('memory_search UX hook integration', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:150880:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:218:      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:150881:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:325:      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151522:  1078	/** Handle memory_context tool — L1 orchestration layer that routes to optimal retrieval strategy.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151536:  1092	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151561:  1117	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151675:  1231	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151694:  1250	  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151762:  1318	  // Phase C: Intent-to-profile auto-routing for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151819:  1375	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151837:  1393	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151948:   554	        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:151960:   566	      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:152007:   218	      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:152009:   220	        tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:152014:   225	          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:152073:   284	      console.warn('[memory_match_triggers] Decay failed:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:152114:   325	      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:152125:   336	      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:154872:- What did not work: CocoIndex was not usable in this run and returned cancelled calls, so I fell back to `rg` plus direct reads; the exact strict validator command still reports `cannot create temp file for here document: Operation not permitted` even though it ends with `RESULT: PASSED`; the phase folder still lacks the Level 3 spec docs the prompt expects, so this remained read-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:154957:- What did not work: CocoIndex was not usable in this run and returned cancelled calls, so I fell back to `rg` plus direct reads; the exact strict validator command still reports `cannot create temp file for here document: Operation not permitted` even though it ends with `RESULT: PASSED`; the phase folder still lacks the Level 3 spec docs the prompt expects, so this remained read-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155012:- What did not work: CocoIndex was not usable in this run and returned cancelled calls, so I fell back to `rg` plus direct reads; the exact strict validator command still reports `cannot create temp file for here document: Operation not permitted` even though it ends with `RESULT: PASSED`; the phase folder still lacks the Level 3 spec docs the prompt expects, so this remained read-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155022:You are a research specialist in persistent memory architectures for AI agents, MCP server design, SQLite/FTS5 search systems, and agent-agnostic tool surfaces. Work like a systems analyst who can trace Go implementation details, separate durable patterns from packaging noise, and turn Engram's design into concrete improvements for `Code_Environment/Public`. Keep the analysis grounded in actual repository evidence, especially around tool profiles, session lifecycle, topic-key stability, passive capture, and search behavior.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155049:`Code_Environment/Public` already has Spec Kit Memory with semantic retrieval via `memory_search`, session continuity via `memory_context`, trigger-based recall via `memory_match_triggers`, causal links, health/status tooling, and context save flows through `generate-context.js`. It also has CocoIndex for semantic code search and code-graph tooling for structural queries. What it does **not** currently have is a first-class session lifecycle API comparable to `mem_session_start` / `mem_session_end`, nor a lightweight MCP tool-profile split equivalent to Engram's `ProfileAgent` versus `ProfileAdmin`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155069:11. Use CocoIndex plus grep to trace implementations and references. If CocoIndex is weak on Go files or times out, fall back to targeted grep plus direct file reads and state that fallback explicitly in the research notes.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155070:12. Compare Engram directly against Public's current memory stack: Spec Kit Memory, `memory_context`, `memory_search`, `memory_match_triggers`, `generate-context.js`, CocoIndex, and any relevant code-graph/session-recovery surfaces. Keep the comparison concrete rather than generic.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155141:- If CocoIndex does not index the Go repo well enough, use grep plus direct file reads and state the fallback explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155175:- explicit comparison against current Public memory capabilities, especially Spec Kit Memory and CocoIndex
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155277:  - Semantic/concept search → `mcp__cocoindex_code__search` (CocoIndex). Skill: `.opencode/skills/mcp-coco-index/`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155291:| **Research/exploration**  | `memory_match_triggers()` → `memory_context()` (unified) OR `memory_search()` (targeted) → Document findings                       |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155292:| **Code search**           | Semantic/concept → `CocoIndex search` · Structural (callers/imports/deps) → `code_graph_query` · Exact text → `Grep` · File paths → `Glob` · Read contents → `Read` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155293:| **Resume prior work**     | `/spec_kit:resume` OR `memory_context({ input: "resume previous work continue session", mode: "resume", profile: "resume", specFolder })` → Review checklist → Continue |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155317:1. **FIRST ACTION** — call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155348:**⚠️ BEFORE using ANY tool (except Gate Actions: memory_match_triggers, skill_advisor.py), you MUST pass all applicable gates below.**
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155354:1. Call `memory_match_triggers(prompt)` → Surface relevant context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155523:allowed-tools: [Read, Write, Edit, Bash, Grep, Glob, Task, WebFetch, memory_context, memory_search]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155744:/bin/zsh -lc 'rg -n "CocoIndex|cancelled|memory_context|memory_search|memory_match_triggers|generate-context|session_bootstrap|code_graph|hybrid-rag-fusion" /Users/michelkerkmeester/.codex/memories/MEMORY.md' in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155754:547:- `memory_stats` currently has no `sessionId` input in tool schema, so calling it after `memory_search` cannot claim the same session by default [Task 2]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155755:548:- verification pattern that worked: confirm fresh `context-server.js` processes, run `session_bootstrap`, execute controlled `memory_search` sequence with fixed session id + trace flags, then query `feedback_events` globally and per-session in sqlite [Task 2]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155757:731:- session_bootstrap, memory_context({mode:"resume",profile:"resume"}), mcp_server/hooks/claude, scripts/hooks/claude, workflow-session-id.vitest.ts, code-graph-query-handler.vitest.ts
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155759:753:## Task 7: Add dedicated README section for CocoIndex + Compact Code Graph with packet references, outcome success
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155761:761:- CocoIndex + Compact Code Graph, README.md, 024-compact-code-graph, 006-documentation-alignment, mcp__cocoindex_code__search, code_graph_query, prettier --check
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155764:786:- `session_bootstrap()` is the primary recovery call for non-hook flows; docs should mention fallback `memory_context({mode:"resume",profile:"resume"})` only after bootstrap guidance [Task 4]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155770:1057:- list_mcp_resources, list_mcp_resource_templates, spec_kit_memory, opencode.json, context-server.js, memory_context, memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:155775:1478:- memory_search cursor, progressive-disclosure, requestQuality, SPECKIT_RESULT_CONFIDENCE_V1, memory-search-ux-hooks.vitest.ts
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156640:I’ve got the MCP profile and store entry points loaded. I’m now cross-checking with semantic search so I can jump straight to the exact lifecycle, topic-key, and passive-capture implementations; if CocoIndex is weak on this Go subtree again, I’ll fall back to `rg` and direct reads and call that out in the report.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156851:/bin/zsh -lc "rg -n \"memory_context|memory_search|memory_match_triggers|generate-context|task_preflight|task_postflight|session_bootstrap|session_resume|memory_health|memory_validate\" /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/dist/memory | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156853:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1263:      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156854:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1264:      : 'memory_search({ query: "last session" })';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156855:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/README.md:93:1. User queries memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156858:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts:224:  //   recovery (0.20)      — A memory_context({ mode: "resume" }) call is the most
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156859:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/shared-memory.ts:250:  // memory_context/memory_match_triggers cannot be wired here yet.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156861:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:7:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156862:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:150:    console.warn('[memory_match_triggers] Failed to fetch memory records:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156863:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:184:/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156864:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:197:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156865:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:218:      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156866:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:220:        tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156867:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:225:          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156868:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:284:      console.warn('[memory_match_triggers] Decay failed:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156869:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:325:      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156870:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:336:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156871:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:374:        console.warn(`[memory_match_triggers] Failed to activate memory ${match.memoryId}:`, message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156872:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:390:          console.warn(`[memory_match_triggers] Co-activation failed for ${memoryId}:`, message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156873:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:491:    console.warn(`[memory_match_triggers] Latency ${latencyMs}ms exceeds 100ms target`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156874:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:511:    tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156875:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:562:const handle_memory_match_triggers = handleMemoryMatchTriggers;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156876:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:565:  handle_memory_match_triggers,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156881:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:42:    toolPattern: /^(read|memory_context|memory_search|memory_list)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156882:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:49:    toolPattern: /^(grep|memory_search)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156897:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:4:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156901:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:312:    'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156902:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:313:    'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156903:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:314:    'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156904:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:181:const key = generateCacheKey('memory_search', { query: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156905:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:184:set(key, searchResults, { toolName: 'memory_search', ttlMs: 30000 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156906:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:196:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156907:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:210:// Automatically clears memory_search, memory_match_triggers, etc.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156909:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:53:  memory_search: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156910:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:55:  memory_context: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156911:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:56:  memory_match_triggers: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156913:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:223:    followUps.push(`Use memory_context with specFolder "${uniqueFolders[0]}" for full context`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156914:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:39:| Tool-Specific Hints | 6 tools | memory_search, checkpoint_restore, memory_save, memory_index_scan, memory_drift_why, memory_causal_link |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156915:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:132:  return buildErrorResponse('memory_search', error, { query });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156916:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:142:const hint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156919:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:433:      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156926:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:222:export const handle_memory_search = lazyFunction(getMemorySearchModule, 'handle_memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156927:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:226:export const handle_memory_match_triggers = lazyFunction(getMemoryTriggersModule, 'handle_memory_match_triggers');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156932:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:320:export const handle_memory_context = lazyFunction(getMemoryContextModule, 'handle_memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156951:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:357:      'Use memory_match_triggers() for prompt-based matching instead'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156952:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:360:    toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156959:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:539:      'Check memory_search() for existing similar content'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156964:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:694:  memory_search: {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156966:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:700:        'Try memory_match_triggers() for trigger-based matching'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156967:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:703:      toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156979:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:123:    nextActions.add('Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` if you need a deeper state refresh.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156992:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:60:// Feature catalog: Unified context retrieval (memory_context)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156993:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:87:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156994:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:124:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156997:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:386:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156998:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:397:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:156999:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1078:/** Handle memory_context tool — L1 orchestration layer that routes to optimal retrieval strategy.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157000:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1092:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157001:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1117:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157002:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1231:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157003:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1250:  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157004:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1318:  // Phase C: Intent-to-profile auto-routing for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157005:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1375:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157006:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1393:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157007:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1471:    tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157008:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1478:      `For more granular control, use L2 tools: memory_search, memory_match_triggers`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157009:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1583:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157010:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1584:      error: 'memory_context failed due to an internal error',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157011:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1606:const handle_memory_context = handleMemoryContext;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157012:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1609:  handle_memory_context,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157013:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:50:    tools: ['memory_context', 'session_resume', 'session_bootstrap']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157014:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:59:    tools: ['memory_search', 'memory_quick_search', 'memory_save', 'memory_match_triggers']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157019:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:52: * Token-pressure policy for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157020:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:60: * Automatic session resume context injection for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157022:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:132:const budget = getTokenBudget('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157023:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:139:const enhanced = enhanceDescription('memory_search', 'Search memories');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157026:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/session-health.ts:128:    hints.push('No tool calls in >60 min. Consider calling `memory_context` to refresh session state.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157027:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:8:// Phase 020: Integrated into memory_context handler for query-intent
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157028:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:977:  // Including it here caused all candidates to be filtered out when memory_context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157029:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:30:      "expectedResultDescription": "Should surface memories about adaptive-fusion.ts (7 intent profiles), intent-classifier.ts, and memory_context intent routing. Cross-document because the behavior spans multiple modules.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157030:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:85:      "query": "memory_context returns wrong results when token pressure is high",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157031:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:251:      "notes": "From T007b Pattern 3: feature description passed to memory_context before implementation."
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157032:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:415:      "query": "the memory_search tool returns stale results after index rebuild",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157033:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:425:      "query": "what is the difference between memory_context and memory_search for context retrieval",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157034:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:430:      "expectedResultDescription": "Should surface both memory_context (L1 unified entry) and memory_search (L2 core) tool schemas and any documentation comparing their use cases.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157037:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:725:      "query": "when should I use memory_search versus memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157039:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:4:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157054:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:175:Packet `026-graph-and-context-optimization/010-fts-capability-cascade-floor` freezes the lexical capability contract that packet `002-implement-cache-warning-hooks` now consumes. `memory_search` responses expose:
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157055:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:48:  liveBaselineResolution: 'code_graph_query' | 'memory_context' | 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157056:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:143:    return 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157057:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:146:  return 'memory_context';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157058:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:162:    if (resolution === 'memory_context_then_grep') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157065:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34:The `pipeline/` directory implements the core retrieval pipeline behind `memory_search`. Each search request flows through four sequential stages, each with a defined I/O contract and clear responsibility boundary. The pipeline supports hybrid, vector and multi-concept search types with optional deep-mode query expansion, cross-encoder reranking, MMR diversity pruning and MPAB chunk-to-parent reassembly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157066:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/enrichment/passive-enrichment.ts:129:      return ['[session] Context quality is CRITICAL. Consider running `memory_context({ mode: "resume" })` or `session_health` to diagnose.'];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157069:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts:90: * reliable retrieval via the `memory_match_triggers` tool. The scoring
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:157075:CocoIndex cancelled again on this Go subtree, so I’m switching to the fallback path the brief allowed: targeted `rg` plus direct source reads. I’m pulling the exact Engram function bodies now, along with the matching Public session/retrieval/health handlers, so the integration-feasibility calls stay code-backed.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158418:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158437:  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158511:/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158524:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158545:      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158547:        tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158552:          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158611:      console.warn('[memory_match_triggers] Decay failed:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158652:      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:158663:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159020:      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159021:      : 'memory_search({ query: "last session" })';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159374:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:218:      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159376:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:225:          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159428:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:123:    nextActions.add('Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` if you need a deeper state refresh.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159815:      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159844:  // ── Sub-call 3: CocoIndex availability (F046/F051: shared helper) ──
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159845:  const cocoIndex: CocoIndexStatus = {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159846:    available: isCocoIndexAvailable(),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:159850:    hints.push('CocoIndex not installed. Install: `bash .opencode/skills/mcp-coco-index/scripts/install.sh`');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161354:  1231	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161373:  1250	  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161441:  1318	  // Phase C: Intent-to-profile auto-routing for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161498:  1375	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161516:  1393	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161583:   184	/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161596:   197	      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161617:   218	      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161619:   220	        tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161624:   225	          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161683:   284	      console.warn('[memory_match_triggers] Decay failed:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161724:   325	      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:161735:   336	      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162026:   433	      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162055:   462	  // ── Sub-call 3: CocoIndex availability (F046/F051: shared helper) ──
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162056:   463	  const cocoIndex: CocoIndexStatus = {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162057:   464	    available: isCocoIndexAvailable(),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162061:   468	    hints.push('CocoIndex not installed. Install: `bash .opencode/skills/mcp-coco-index/scripts/install.sh`');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162288:  1263	      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162289:  1264	      : 'memory_search({ query: "last session" })';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162329:   547	- `memory_stats` currently has no `sessionId` input in tool schema, so calling it after `memory_search` cannot claim the same session by default [Task 2]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162330:   548	- verification pattern that worked: confirm fresh `context-server.js` processes, run `session_bootstrap`, execute controlled `memory_search` sequence with fixed session id + trace flags, then query `feedback_events` globally and per-session in sqlite [Task 2]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162339:   786	- `session_bootstrap()` is the primary recovery call for non-hook flows; docs should mention fallback `memory_context({mode:"resume",profile:"resume"})` only after bootstrap guidance [Task 4]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162373:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:184:/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:162963:- **What it does**: Engram persists session rows explicitly and exposes start/end as first-class tools. Public already has richer session orchestration through trusted session IDs, `memory_context`, `session_resume`, and `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163007:- What did not work: CocoIndex cancelled again on the Go subtree, so this iteration relied on `rg` plus direct reads; the exact strict validator command still emitted `cannot create temp file for here document: Operation not permitted`, but it finished with `RESULT: PASSED`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163040:- **What it does**: Engram persists session rows explicitly and exposes start/end as first-class tools. Public already has richer session orchestration through trusted session IDs, `memory_context`, `session_resume`, and `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163084:- What did not work: CocoIndex cancelled again on the Go subtree, so this iteration relied on `rg` plus direct reads; the exact strict validator command still emitted `cannot create temp file for here document: Operation not permitted`, but it finished with `RESULT: PASSED`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163093:- **What it does**: Engram persists session rows explicitly and exposes start/end as first-class tools. Public already has richer session orchestration through trusted session IDs, `memory_context`, `session_resume`, and `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163137:- What did not work: CocoIndex cancelled again on the Go subtree, so this iteration relied on `rg` plus direct reads; the exact strict validator command still emitted `cannot create temp file for here document: Operation not permitted`, but it finished with `RESULT: PASSED`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163147:You are a research specialist in persistent memory architectures for AI agents, MCP server design, SQLite/FTS5 search systems, and agent-agnostic tool surfaces. Work like a systems analyst who can trace Go implementation details, separate durable patterns from packaging noise, and turn Engram's design into concrete improvements for `Code_Environment/Public`. Keep the analysis grounded in actual repository evidence, especially around tool profiles, session lifecycle, topic-key stability, passive capture, and search behavior.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163174:`Code_Environment/Public` already has Spec Kit Memory with semantic retrieval via `memory_search`, session continuity via `memory_context`, trigger-based recall via `memory_match_triggers`, causal links, health/status tooling, and context save flows through `generate-context.js`. It also has CocoIndex for semantic code search and code-graph tooling for structural queries. What it does **not** currently have is a first-class session lifecycle API comparable to `mem_session_start` / `mem_session_end`, nor a lightweight MCP tool-profile split equivalent to Engram's `ProfileAgent` versus `ProfileAdmin`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163194:11. Use CocoIndex plus grep to trace implementations and references. If CocoIndex is weak on Go files or times out, fall back to targeted grep plus direct file reads and state that fallback explicitly in the research notes.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163195:12. Compare Engram directly against Public's current memory stack: Spec Kit Memory, `memory_context`, `memory_search`, `memory_match_triggers`, `generate-context.js`, CocoIndex, and any relevant code-graph/session-recovery surfaces. Keep the comparison concrete rather than generic.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163266:- If CocoIndex does not index the Go repo well enough, use grep plus direct file reads and state the fallback explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163300:- explicit comparison against current Public memory capabilities, especially Spec Kit Memory and CocoIndex
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163470:- **CocoIndex Code MCP** — semantic code search. MUST use when exploring unfamiliar code, finding implementations by concept/intent, or when Grep/Glob exact matching is insufficient. Skill: `.opencode/skills/mcp-coco-index/`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163485:  |     YES --> CocoIndex search (semantic)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163490:        YES --> CocoIndex search FIRST, then Grep/Glob to fill gaps
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163493:CocoIndex triggers: "find code that does X", "how is X implemented", "where is the logic for X", "similar code", "find patterns", exploring unfamiliar modules, any intent-based query where exact tokens are unknown.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163497:| **MCP tool** | `search(query, languages, paths, num_results, refresh_index)` | AI agent integration |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163511:3. If the graph remains unavailable, fall back to CocoIndex + direct file reads
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163553:| **Research/exploration**  | `memory_match_triggers()` → `memory_context()` (unified) OR `memory_search()` (targeted) → Document findings                       |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163554:| **Code search**           | CocoIndex for semantic/intent → Grep for exact text → Glob for file paths → Read for contents                                       |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163555:| **Resume prior work**     | `/spec_kit:resume` OR `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` → Review → Continue    |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163577:**⚠️ BEFORE using ANY tool (except Gate Actions: memory_match_triggers, skill_advisor.py), you MUST pass all applicable gates below.**
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163583:1. Call `memory_match_triggers(prompt)` → Surface relevant context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163737:  - Semantic/concept search → `mcp__cocoindex_code__search` (CocoIndex). Skill: `.opencode/skills/mcp-coco-index/`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163751:| **Research/exploration**  | `memory_match_triggers()` → `memory_context()` (unified) OR `memory_search()` (targeted) → Document findings                       |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163752:| **Code search**           | Semantic/concept → `CocoIndex search` · Structural (callers/imports/deps) → `code_graph_query` · Exact text → `Grep` · File paths → `Glob` · Read contents → `Read` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163753:| **Resume prior work**     | `/spec_kit:resume` OR `memory_context({ input: "resume previous work continue session", mode: "resume", profile: "resume", specFolder })` → Review checklist → Continue |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163777:1. **FIRST ACTION** — call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163808:**⚠️ BEFORE using ANY tool (except Gate Actions: memory_match_triggers, skill_advisor.py), you MUST pass all applicable gates below.**
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163814:1. Call `memory_match_triggers(prompt)` → Surface relevant context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:163947:allowed-tools: [Read, Write, Edit, Bash, Grep, Glob, Task, WebFetch, memory_context, memory_search]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164240:CocoIndex cancelled again on both the Go subtree and the Public handlers, which matches the earlier note. I’m switching to targeted `rg` plus direct reads so the findings stay code-backed instead of speculative.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164488:/bin/zsh -lc 'rg -n "session_bootstrap|session_resume|memory_context|memory_search|memory_match_triggers|generate-context|trusted session|sessionId|resolveSession|session_start|session_end|bootstrap|session-manager|memory_save|memory_validate|POST-SAVE|save/markdown-evidence-builder|context-server" .opencode/skills/system-spec-kit/mcp_server .opencode/skills/system-spec-kit/scripts/dist/memory/generate-context.js' in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164518:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:759:    'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164519:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:760:    'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164521:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:772:        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164530:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:882:    if (name === 'memory_context' && args.mode === 'resume') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164532:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:912:      name === 'memory_context' && args.mode === 'resume';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164536:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:964:    if (name !== 'memory_search' && name !== 'memory_context' && name !== 'memory_quick_search' && name !== 'session_health') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164537:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:977:    if ((name === 'memory_search' || name === 'memory_context') && result && !result.isError && result.content?.[0]?.text) {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164637:.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:229:| `SPECKIT_PRESSURE_POLICY` | `true` | boolean | Token-pressure policy for memory_context responses. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164638:.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:230:| `SPECKIT_AUTO_RESUME` | `true` | boolean | Automatic session resume context injection for memory_context. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164640:.opencode/skills/system-spec-kit/mcp_server/handlers/shared-memory.ts:250:  // memory_context/memory_match_triggers cannot be wired here yet.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164643:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:7:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164647:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:150:    console.warn('[memory_match_triggers] Failed to fetch memory records:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164648:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:184:/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164649:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:197:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164652:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:218:      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164653:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:220:        tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164654:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:225:          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164658:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:284:      console.warn('[memory_match_triggers] Decay failed:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164659:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:325:      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164660:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:336:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164663:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:374:        console.warn(`[memory_match_triggers] Failed to activate memory ${match.memoryId}:`, message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164664:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:390:          console.warn(`[memory_match_triggers] Co-activation failed for ${memoryId}:`, message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164667:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:491:    console.warn(`[memory_match_triggers] Latency ${latencyMs}ms exceeds 100ms target`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164669:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:511:    tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164671:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:562:const handle_memory_match_triggers = handleMemoryMatchTriggers;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164672:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:565:  handle_memory_match_triggers,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164700:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:426:- `memory_context` (unified context retrieval)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164701:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:427:- `memory_search` (semantic search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164702:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:428:- `memory_match_triggers` (fast trigger matching)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164708:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:465:- [ ] `memory_search()` returns results (or empty if no memories are indexed yet)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164709:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:530:### memory_context: Unified Context Retrieval
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164710:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:532:`memory_context()` is the primary entry point for context loading. It detects task intent and routes to the optimal retrieval strategy automatically.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164711:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:548:### memory_search: Semantic Search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164712:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:550:`memory_search()` runs vector-based similarity search across all indexed memories.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164713:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:559:### memory_match_triggers: Fast Keyword Lookup
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164714:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:561:`memory_match_triggers()` provides sub-50ms keyword-based matching. Use it for immediate context surfacing at the start of a conversation.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164717:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:629:- `ContextEnvelope`: Wraps all `memory_context()` responses with metadata (mode used, memories returned, intent detected)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164719:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:681:**Behind the scenes:** The AI calls `memory_context()` with `mode: "resume"` and `anchors: ["state", "next-steps"]`, then returns the previous session state.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164720:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:692:1. AI calls `memory_context({ input: "add user profiles", mode: "auto" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164726:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1047:MCP TOOLS: memory_context, memory_search, memory_match_triggers,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164728:.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1064:| v1.7.x | 2026-02-20 | Cross-encoder reranking enabled by default. Co-activation score boost fix. Query expansion on deep mode. Evidence gap warnings. MMR reranking with intent-mapped lambda. Phase system support (recursive validation, phase detection scoring). Feature flag updates. `memory_context` tokenUsage parameter. 28-tool surface area. |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164751:.opencode/skills/system-spec-kit/mcp_server/handlers/session-health.ts:128:    hints.push('No tool calls in >60 min. Consider calling `memory_context` to refresh session state.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164780:.opencode/skills/system-spec-kit/mcp_server/README.md:9:  - "memory_context"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164781:.opencode/skills/system-spec-kit/mcp_server/README.md:10:  - "memory_search"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164786:.opencode/skills/system-spec-kit/mcp_server/README.md:200:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164788:.opencode/skills/system-spec-kit/mcp_server/README.md:547:**Query routing:** Structural queries (callers, imports, dependencies) go to `code_graph_query`. Semantic and concept queries go to CocoIndex (`mcp__cocoindex_code__search`). Session and memory queries go to `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164789:.opencode/skills/system-spec-kit/mcp_server/README.md:557:**Start here for most tasks**: `memory_context` (L1) automatically figures out what you need. Use the lower-level tools when you want precise control.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164790:.opencode/skills/system-spec-kit/mcp_server/README.md:563:##### `memory_context`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164792:.opencode/skills/system-spec-kit/mcp_server/README.md:587:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164794:.opencode/skills/system-spec-kit/mcp_server/README.md:601:Resume session with combined memory, code graph and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. The response carries freshness-aware code-graph status (`fresh`, `stale`, `empty`, `error`) instead of count-only health. For the canonical first-call recovery path on session start or after `/clear`, prefer `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164798:.opencode/skills/system-spec-kit/mcp_server/README.md:622:##### `memory_search`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164799:.opencode/skills/system-spec-kit/mcp_server/README.md:646:  "tool": "memory_search",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164800:.opencode/skills/system-spec-kit/mcp_server/README.md:674:##### `memory_match_triggers`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164801:.opencode/skills/system-spec-kit/mcp_server/README.md:688:  "tool": "memory_match_triggers",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164810:.opencode/skills/system-spec-kit/mcp_server/README.md:1326:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164815:.opencode/skills/system-spec-kit/mcp_server/README.md:1538:| Find a past decision | `memory_context` | Set `intent: "find_decision"` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164816:.opencode/skills/system-spec-kit/mcp_server/README.md:1539:| Search for specific terms | `memory_search` | Use `concepts: ["term1", "term2"]` for AND search |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164817:.opencode/skills/system-spec-kit/mcp_server/README.md:1540:| Check triggers on every prompt | `memory_match_triggers` | Pass the user's prompt text |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164819:.opencode/skills/system-spec-kit/mcp_server/README.md:1556:**What you see**: Irrelevant or low-scoring results from `memory_search` or `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164820:.opencode/skills/system-spec-kit/mcp_server/README.md:1567:{ "tool": "memory_search", "arguments": { "query": "your query", "min_quality_score": 0.5 } }
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164824:.opencode/skills/system-spec-kit/mcp_server/README.md:1717:Start with `memory_context` for all retrieval tasks. It handles intent detection and routing automatically. Use `memory_search` when you want explicit control over channels. Use `memory_match_triggers` when processing a raw prompt at the start of each turn. Use L4-L7 tools only for mutation, analysis or maintenance.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164866:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:42:  name: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164867:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:44:  inputSchema: { type: 'object', additionalProperties: false, properties: { input: { type: 'string', minLength: 1, description: 'The query, prompt, or context description (required)' }, mode: { type: 'string', enum: ['auto', 'quick', 'deep', 'focused', 'resume'], default: 'auto', description: 'Context retrieval mode: auto (detect intent), quick (fast triggers), deep (comprehensive search), focused (intent-optimized), resume (session recovery)' }, intent: { type: 'string', enum: ['add_feature', 'fix_bug', 'refactor', 'security_audit', 'understand', 'find_spec', 'find_decision'], description: 'Explicit task intent. If not provided and mode=auto, intent is auto-detected from input.' }, specFolder: { type: 'string', description: 'Limit context to specific spec folder' }, tenantId: { type: 'string', description: 'Tenant boundary for governed retrieval when memory_context routes to memory_search.' }, userId: { type: 'string', description: 'User boundary for governed retrieval when memory_context routes to memory_search.' }, agentId: { type: 'string', description: 'Agent boundary for governed retrieval when memory_context routes to memory_search.' }, sharedSpaceId: { type: 'string', description: 'Shared-space boundary for governed retrieval when memory_context routes to memory_search.' }, limit: { type: 'number', minimum: 1, maximum: 100, description: 'Maximum results (mode-specific defaults apply)' }, sessionId: { type: 'string', description: 'Optional server-issued session identifier for working-memory continuity. When provided, it must match an existing server-managed session or the call is rejected. Omit it to let the server generate a new session for this request.' }, enableDedup: { type: 'boolean', default: true, description: 'Enable session deduplication' }, includeContent: { type: 'boolean', default: false, description: 'Include full file content in results' }, includeTrace: { type: 'boolean', default: false, description: 'Include provenance-rich trace data (scores, source, trace) in results when underlying memory_search is called' }, tokenUsage: { type: 'number', minimum: 0.0, maximum: 1.0, description: "Optional caller token usage ratio (0.0-1.0)" }, anchors: { type: 'array', items: { type: 'string' }, description: 'Filter content to specific anchors (e.g., ["state", "next-steps"] for resume mode)' }, profile: { type: 'string', enum: ['quick', 'research', 'resume', 'debug'], description: 'Optional response profile formatter. Returns a reduced or mode-aware response shape when profile formatting is enabled.' } }, required: ['input'] },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164868:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:49:  name: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164871:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:190:// E3: Simplified search — 3 params, sensible defaults, delegates to memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164872:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:193:  description: '[L2:Core] Simplified search — query + optional limit + optional spec folder. Delegates to memory_search with sensible defaults (intent auto-detect ON, dedup ON, content included, limit 10). Use this when you want fast search without configuring 31 parameters.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164873:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:211:  name: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164882:.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:741:  description: '[L1:Orchestration] Resume session with combined memory, code graph, and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. For the canonical first-call recovery path on session start or after /clear, prefer session_bootstrap. Use minimal: true to skip the heavy memory context call and return code graph, CocoIndex, structural context, hints, and session-quality metadata without the full memory payload.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164894:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:100:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164898:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:340:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164905:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:482:/** Handle memory_search tool — performs hybrid vector/BM25 search with intent-aware ranking.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164909:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:554:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164910:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:566:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164911:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:594:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164912:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:613:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164913:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:625:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164916:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:751:  const cacheKey = toolCache.generateCacheKey('memory_search', cacheArgs);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164922:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1044:      toolCache.set(cacheKey, cachePayload, { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164935:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1374:const handle_memory_search = handleMemorySearch;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164936:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1377:  handle_memory_search,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164948:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:112:  includeTrace: z.boolean().optional(), // CHK-040: Forward to internal memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164955:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:397:  memory_context: memoryContextSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164956:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:398:  memory_search: memorySearchSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164957:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:400:  memory_match_triggers: memoryMatchTriggersSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164962:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:462:  memory_context: ['input', 'mode', 'intent', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'sessionId', 'enableDedup', 'includeContent', 'includeTrace', 'tokenUsage', 'anchors', 'profile'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164963:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:463:  memory_search: ['cursor', 'query', 'concepts', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'sessionId', 'enableDedup', 'tier', 'contextType', 'useDecay', 'includeContiguity', 'includeConstitutional', 'enableSessionBoost', 'enableCausalBoost', 'includeContent', 'anchors', 'min_quality_score', 'minQualityScore', 'bypassCache', 'rerank', 'applyLengthPenalty', 'applyStateLimits', 'minState', 'intent', 'autoDetectIntent', 'trackAccess', 'includeArchived', 'mode', 'includeTrace', 'profile'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164964:.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:465:  memory_match_triggers: ['prompt', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'session_id', 'turnNumber', 'include_cognitive'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164976:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:86:  'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164977:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:87:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164978:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:89:  'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164989:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:460:    recommendedCalls.push('memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164990:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:463:    recommendedCalls.push('memory_match_triggers({ prompt: "<your task>" })');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:164992:.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:482:      graphRetrieval: 'For broad topic questions, use memory_search with retrievalLevel: "global" for community-level results. For specific memories, use "local" (default). Use "auto" for automatic fallback.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165015:.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:433:      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165025:.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts:90: * reliable retrieval via the `memory_match_triggers` tool. The scoring
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165034:.opencode/skills/system-spec-kit/mcp_server/hooks/README.md:70:- `MEMORY_AWARE_TOOLS` currently includes `memory_context`, `memory_search`, `memory_match_triggers`, `memory_list`, `memory_save`, and `memory_index_scan`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165037:.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:222:export const handle_memory_search = lazyFunction(getMemorySearchModule, 'handle_memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165038:.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:226:export const handle_memory_match_triggers = lazyFunction(getMemoryTriggersModule, 'handle_memory_match_triggers');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165041:.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:320:export const handle_memory_context = lazyFunction(getMemoryContextModule, 'handle_memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165143:.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1263:      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165144:.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1264:      : 'memory_search({ query: "last session" })';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165161:.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:123:    nextActions.add('Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` if you need a deeper state refresh.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165180:.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:4:// Dispatch for L1 Orchestration tool: memory_context (T303).
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165181:.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:11:export const TOOL_NAMES = new Set(['memory_context']);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165182:.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:16:    case 'memory_context': return handleMemoryContext(parseArgs<ContextArgs>(validateToolArgs('memory_context', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165187:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:50:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165189:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:61:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165190:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:77:      content: 'Context was compacted and auto-recovered from the cached compact brief. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165193:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:140:        '- `memory_context({ input, mode })` — unified context retrieval',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165194:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:141:        '- `memory_match_triggers({ prompt })` — fast trigger matching',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165195:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:142:        '- `memory_search({ query })` — semantic search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165198:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:185:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165199:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:190:      content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165200:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:202:      content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165207:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:60:// Feature catalog: Unified context retrieval (memory_context)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165209:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:87:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165211:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:124:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165214:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:386:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165215:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:397:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165222:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1078:/** Handle memory_context tool — L1 orchestration layer that routes to optimal retrieval strategy.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165223:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1092:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165224:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1117:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165226:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1231:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165229:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1250:  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165231:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1318:  // Phase C: Intent-to-profile auto-routing for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165232:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1375:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165233:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1393:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165234:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1471:    tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165235:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1478:      `For more granular control, use L2 tools: memory_search, memory_match_triggers`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165236:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1583:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165237:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1584:      error: 'memory_context failed due to an internal error',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165238:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1606:const handle_memory_context = handleMemoryContext;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165239:.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1609:  handle_memory_context,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165245:.opencode/skills/system-spec-kit/mcp_server/lib/session/README.md:93:1. User queries memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165270:.opencode/skills/system-spec-kit/mcp_server/tools/README.md:27:- `context-tools.ts` - dispatch for `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165271:.opencode/skills/system-spec-kit/mcp_server/tools/README.md:40:- `memory-tools.ts` implements the `memory_quick_search` delegation path by building a richer `memory_search` request and relabeling the returned envelope metadata back to `memory_quick_search`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165275:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:62:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165276:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:64:  'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165279:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:78:    case 'memory_search':         return handleMemorySearch(parseArgs<SearchArgs>(validateToolArgs('memory_search', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165280:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:80:      // E3: Delegate to memory_search with sensible defaults
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165281:.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:99:    case 'memory_match_triggers': return handleMemoryMatchTriggers(parseArgs<TriggerArgs>(validateToolArgs('memory_match_triggers', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165351:.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts:224:  //   recovery (0.20)      — A memory_context({ mode: "resume" }) call is the most
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165352:.opencode/skills/system-spec-kit/mcp_server/hooks/claude/README.md:31:Hooks are transport reliability, not separate business logic. They call the same retrieval primitives (`memory_match_triggers`, `memory_context`) that other runtimes call explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165359:.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:416:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165360:.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:709:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165365:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:51:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165366:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:62:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165367:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:73:      content: 'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165368:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:106:        '- `memory_context({ input, mode })` - unified context retrieval',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165369:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:107:        '- `memory_match_triggers({ prompt })` - fast trigger matching',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165370:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:108:        '- `memory_search({ query })` - semantic search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165373:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:149:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165374:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:155:    content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165375:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:163:    content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165471:.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:175:Packet `026-graph-and-context-optimization/010-fts-capability-cascade-floor` freezes the lexical capability contract that packet `002-implement-cache-warning-hooks` now consumes. `memory_search` responses expose:
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165477:.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/compact-inject.ts:63:    'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165480:.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:23:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165485:.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:384:  it('C13: Response meta.tool is memory_search', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165486:.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:388:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165529:.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:482:describe('T059: autoDetectIntent Parameter (memory_search)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165571:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:59:    it('T516-2: handle_memory_search alias is exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165572:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:60:      expect(typeof handler.handle_memory_search).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165595:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:83:      validateToolInputSchema('memory_context', {}, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165596:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:119:      validateToolInputSchema('memory_context', { input: 'resume', mode: 'invalid-mode' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165597:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:133:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165598:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:137:    expect(errorSpy.mock.calls.some((call) => String(call[0]).includes('[schema-validation] memory_search:'))).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165599:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:240:   4. memory_search LIMIT CONTRACT (schema + runtime alignment)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165600:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:243:describe('memory_search limit contract', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165601:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:246:      validateToolInputSchema('memory_search', { cursor: 'opaque-cursor-token' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165602:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:252:      validateToolArgs('memory_search', { cursor: 'opaque-cursor-token' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165603:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:258:      validateToolInputSchema('memory_search', { concepts: ['alpha', 'beta'] }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165604:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:264:      validateToolInputSchema('memory_search', {}, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165605:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:270:      validateToolArgs('memory_search', { query: 'ab', limit: 100 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165606:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:276:      validateToolArgs('memory_search', { query: 'ab', limit: 101 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165607:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:282:      validateToolInputSchema('memory_search', { query: 'ab', limit: 101 }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165608:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:288:      validateToolArgs('memory_search', { concepts: ['solo'] });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165609:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:292:  it('public schema rejects unknown memory_search parameters', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165610:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:294:      validateToolInputSchema('memory_search', { query: 'valid query', unexpected: true }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165611:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:300:      validateToolInputSchema('memory_search', { query: 'a' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165612:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:304:  it('runtime rejects unknown memory_search parameters', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165613:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:306:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165614:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:310:  it('runtime accepts governed scope fields for memory_search', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165615:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:312:      validateToolArgs('memory_search', {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165616:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:322:  it('public and runtime schemas accept response profiles for memory_search', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165617:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:329:      validateToolInputSchema('memory_search', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165618:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:331:    expect(validateToolArgs('memory_search', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165619:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:336:  it('public and runtime schemas accept governed scope fields for memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165620:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:346:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165621:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:348:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165622:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:351:  it('public and runtime schemas accept response profiles for memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165623:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:358:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165624:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:360:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165625:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:378:  it('public and runtime schemas accept governed scope fields for memory_match_triggers', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165626:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:389:      validateToolInputSchema('memory_match_triggers', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165627:.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:391:    expect(validateToolArgs('memory_match_triggers', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165636:.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:42:    toolPattern: /^(read|memory_context|memory_search|memory_list)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165637:.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:49:    toolPattern: /^(grep|memory_search)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165647:.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:977:  // Including it here caused all candidates to be filtered out when memory_context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165666:.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:52: * Token-pressure policy for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165667:.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:60: * Automatic session resume context injection for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165683:.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:4:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165687:.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34:The `pipeline/` directory implements the core retrieval pipeline behind `memory_search`. Each search request flows through four sequential stages, each with a defined I/O contract and clear responsibility boundary. The pipeline supports hybrid, vector and multi-concept search types with optional deep-mode query expansion, cross-encoder reranking, MMR diversity pruning and MPAB chunk-to-parent reassembly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165691:.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:4:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165751:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:76:    it('T517-2: handle_memory_match_triggers alias exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165752:.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:77:      expect(typeof handler.handle_memory_match_triggers).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165776:.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:53:  memory_search: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165777:.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:55:  memory_context: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165778:.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:56:  memory_match_triggers: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165780:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:6:  { tool: 'memory_context', handler: 'handleMemoryContext', layer: 'L1' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165781:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:7:  { tool: 'memory_search', handler: 'handleMemorySearch', layer: 'L2' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165782:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:8:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers', layer: 'L2' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165785:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:33:  { camel: 'handleMemorySearch', snake: 'handle_memory_search' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165786:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:34:  { camel: 'handleMemoryMatchTriggers', snake: 'handle_memory_match_triggers' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165789:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:56:  { camel: 'handleMemoryContext', snake: 'handle_memory_context' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165790:.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:39:| Tool-Specific Hints | 6 tools | memory_search, checkpoint_restore, memory_save, memory_index_scan, memory_drift_why, memory_causal_link |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165791:.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:132:  return buildErrorResponse('memory_search', error, { query });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165792:.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:142:const hint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165827:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:357:      'Use memory_match_triggers() for prompt-based matching instead'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165828:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:360:    toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165834:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:539:      'Check memory_search() for existing similar content'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165838:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:694:  memory_search: {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165839:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:700:        'Try memory_match_triggers() for trigger-based matching'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165840:.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:703:      toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165846:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:82:      const key1 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165847:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:83:      const key2 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165848:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:88:      const key1 = generateCacheKey('memory_search', { query: 'auth' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165849:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:89:      const key2 = generateCacheKey('memory_search', { query: 'login' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165850:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:95:      const key1 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165852:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:352:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165853:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:353:      const key2 = generateCacheKey('memory_search', { query: 'test2' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165855:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:355:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165856:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:356:      set(key2, 'value2', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165858:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:358:      const invalidated = invalidateByTool('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165859:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:366:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165861:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:369:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165863:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:380:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165865:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:383:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165867:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:394:      const searchKey = generateCacheKey('memory_search', { query: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165868:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:395:      const triggerKey = generateCacheKey('memory_match_triggers', { prompt: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165869:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:396:      set(searchKey, 'search_result', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165870:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:397:      set(triggerKey, 'trigger_result', { toolName: 'memory_match_triggers' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165871:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:423:      const key = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165872:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:427:        'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165873:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:436:      expect(invalidateByTool('memory_search')).toBe(0);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165874:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:439:      const second = withCache('memory_search', args, async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165875:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:589:      const key = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165876:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:593:        'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165877:.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:603:      const second = withCache('memory_search', args, async () => 'fresh-after-shutdown');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165892:.opencode/skills/system-spec-kit/mcp_server/tests/tiered-injection-turnNumber.vitest.ts:183:      expect(typeof handlerExports.handle_memory_match_triggers).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165898:.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:18:        memory_context: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165899:.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:19:        memory_search: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165901:.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:21:        memory_match_triggers: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165908:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:1:// TEST: memory_context per-channel eval logging (T056)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165909:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:88:describe('T056: memory_context emits per-strategy channel eval rows', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165910:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:30:      "expectedResultDescription": "Should surface memories about adaptive-fusion.ts (7 intent profiles), intent-classifier.ts, and memory_context intent routing. Cross-document because the behavior spans multiple modules.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165911:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:85:      "query": "memory_context returns wrong results when token pressure is high",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165912:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:251:      "notes": "From T007b Pattern 3: feature description passed to memory_context before implementation."
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165913:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:415:      "query": "the memory_search tool returns stale results after index rebuild",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165914:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:425:      "query": "what is the difference between memory_context and memory_search for context retrieval",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165915:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:430:      "expectedResultDescription": "Should surface both memory_context (L1 unified entry) and memory_search (L2 core) tool schemas and any documentation comparing their use cases.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165919:.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:725:      "query": "when should I use memory_search versus memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165936:.opencode/skills/system-spec-kit/mcp_server/tests/review-fixes.vitest.ts:41:    const result = validateToolArgs('memory_search', {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165967:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:159:      'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165968:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:160:      'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165969:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:162:      'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165977:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:292:      'memory_context', 'memory_search', 'memory_quick_search', 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165989:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:927:        { id: 'call-1', params: { name: 'memory_search', arguments: {} } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165990:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:944:      expect(callArgs[0]).toBe('memory_search')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165991:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1054:              name: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165993:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1103:        memoryAwareTools: new Set<string>(['memory_search']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165994:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1113:        { id: 'call-5', params: { name: 'memory_search', arguments: { query: 'hook validation' } } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165995:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1123:    it('T000g: memory_context resume mode invokes TM-05 compaction hook at runtime', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165996:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1131:        memoryAwareTools: new Set<string>(['memory_context']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165997:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1144:          params: { name: 'memory_context', arguments: { input: 'session resume context', mode: 'resume' } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165998:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1157:    it('T000h: memory_context non-resume mode keeps SK-004 memory-aware path', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:165999:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1164:        memoryAwareTools: new Set<string>(['memory_context']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166000:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1177:          params: { name: 'memory_context', arguments: { input: 'focused retrieval context', mode: 'focused' } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166003:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1563:      const response = errorsModule!.buildErrorResponse!('memory_search', testError, { query: 'test' })
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166004:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1581:      const hint = errorsModule!.getRecoveryHint!('memory_search', 'UNKNOWN_TOOL')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166005:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1614:    it('T28: L1 budget = 3500 (memory_context)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166006:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1619:      expect(layerDefs!.getTokenBudget!('memory_context')).toBe(3500)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166007:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1622:    it('T28b: L2 budget = 3500 (memory_search)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166008:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1627:      expect(layerDefs!.getTokenBudget!('memory_search')).toBe(3500)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166009:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1703:    const expectedAwareTools = ['memory_context', 'memory_search', 'memory_match_triggers', 'memory_list', 'memory_save', 'memory_index_scan']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166012:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2084:      'memory_context': '[L1:Orchestration]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166013:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2085:      'memory_search': '[L2:Core]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166014:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2086:      'memory_match_triggers': '[L2:Core]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166017:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2131:    it('T000e: memory_context supports optional tokenUsage (0.0-1.0)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166018:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2132:      expect(toolSchemasCode).toMatch(/name:\s*'memory_context'[\s\S]*?tokenUsage:\s*\{\s*type:\s*'number'/)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166021:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2315:        'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166022:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2341:      expect(result).toContain('memory_context')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166023:.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2342:      expect(result).toContain('memory_search')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166025:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:48:  liveBaselineResolution: 'code_graph_query' | 'memory_context' | 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166026:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:143:    return 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166027:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:146:  return 'memory_context';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166028:.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:162:    if (resolution === 'memory_context_then_grep') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166069:.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:1:// TEST: memory_search per-channel eval logging (T056)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166070:.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:106:describe('T056: memory_search emits per-channel eval rows', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166071:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:117:        memory_context: 'L1',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166072:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:118:        memory_search: 'L2',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166074:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:120:        memory_match_triggers: 'L2',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166076:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:194:        { tool: 'memory_context', expected: '[L1:Orchestration]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166077:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:195:        { tool: 'memory_search', expected: '[L2:Core]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166078:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:221:      const result = mod.enhanceDescription('memory_context', 'Some description text');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166079:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:227:        { tool: 'memory_search', desc: 'Search memories', prefix: '[L2:Core]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166080:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:242:      expect(mod.enhanceDescription('memory_context', '')).toBe('[L1:Orchestration] ');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166081:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:252:        { tool: 'memory_context', expected: 3500 },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166082:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:253:        { tool: 'memory_search', expected: 3500 },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166083:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:270:      expect(typeof mod.getTokenBudget('memory_context')).toBe('number');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166084:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:280:      const info = expectLayerInfo(mod.getLayerInfo('memory_context'));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166085:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:287:      expect(info.tools).toContain('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166086:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:291:      const info1 = mod.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166087:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:292:      const info2 = mod.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166088:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:301:      const info = expectLayerInfo(mod.getLayerInfo('memory_search'));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166089:.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:430:      const toolSamples = ['memory_context', 'memory_search', 'memory_list',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166090:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:50:    tools: ['memory_context', 'session_resume', 'session_bootstrap']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166091:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:59:    tools: ['memory_search', 'memory_quick_search', 'memory_save', 'memory_match_triggers']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166103:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:132:const budget = getTokenBudget('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166104:.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:139:const enhanced = enhanceDescription('memory_search', 'Search memories');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166123:.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:250:  it('T020-02: Generates memory_search command with sessionId when specFolder is not provided', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166124:.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:254:  it('T020-03: Generates generic memory_search when neither specFolder nor sessionId is provided', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166126:.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:50:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166127:.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:68:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166128:.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:83:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166134:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:181:  it('T022: memory_search has tool-specific hints', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166135:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:182:    expect(TOOL_SPECIFIC_HINTS.memory_search).toBeDefined();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166136:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:183:    expect(typeof TOOL_SPECIFIC_HINTS.memory_search).toBe('object');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166140:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:221:  it('T029: memory_search EMBEDDING_FAILED has contextual hint', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166141:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:224:      TOOL_SPECIFIC_HINTS.memory_search?.[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166144:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:244:    const searchHint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166145:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:246:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166148:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:301:      'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166149:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:315:    const hasSearch = hasSpecificHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166150:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:356:    const searchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166151:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:362:    const searchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166152:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:365:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166153:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:669:  it('T087: QUERY_TOO_LONG suggests memory_match_triggers()', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166154:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:672:      a.includes('memory_match_triggers()')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166155:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:713:    const toolSpecific = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166156:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:718:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166157:.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:725:    const allSearchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166158:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:86:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166162:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:30:    tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166163:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:37:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166164:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:43:    tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166167:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:176:  { tool: 'memory_context', handler: 'handleMemoryContext' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166168:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:177:  { tool: 'memory_search', handler: 'handleMemorySearch' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166170:.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:179:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166171:.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:133:    expect(matchRule('memory_search', 'spec.md error context')).not.toBeNull();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166172:.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:134:    expect(matchRule('memory_context', 'spec.md metadata')).not.toBeNull();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166196:.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:223:    followUps.push(`Use memory_context with specFolder "${uniqueFolders[0]}" for full context`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166197:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:20:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166200:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:58:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166201:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:97:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166202:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:108:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166203:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:135:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166204:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:143:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166205:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:152:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166207:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:186:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166209:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:206:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166210:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:254:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166211:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:312:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166212:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:352:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166213:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:363:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166214:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:373:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166215:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:384:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166216:.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:409:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166220:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:181:const key = generateCacheKey('memory_search', { query: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166221:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:184:set(key, searchResults, { toolName: 'memory_search', ttlMs: 30000 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166222:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:196:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166224:.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:210:// Automatically clears memory_search, memory_match_triggers, etc.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166225:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:287:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166226:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:296:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166227:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:302:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166228:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:310:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166229:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:311:    expect(resp.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166230:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:318:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166231:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:328:  it('F7: Tool-specific hints included for memory_search + E001', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166232:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:330:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166233:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:353:    const err = createErrorWithHint('E040', 'fail', {}, 'memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166234:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:469:  it('K2: Has memory_search, checkpoint_restore, memory_save', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166235:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:470:    expect('memory_search' in TOOL_SPECIFIC_HINTS).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166237:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:476:    const searchHints = TOOL_SPECIFIC_HINTS['memory_search'];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166238:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:492:  it('L1: Returns tool-specific hint for memory_search + E001', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166239:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:493:    const hint = getRecoveryHint('memory_search', 'E001');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166240:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:512:    const hint = getRecoveryHint('memory_search', 'E040');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166241:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:524:  it('M1: Returns true for known tool+code (memory_search, E001)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166242:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:525:    expect(hasSpecificHint('memory_search', 'E001')).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166243:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:543:    const hints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166244:.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:550:    const hints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166270:.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:312:    'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166271:.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:313:    'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166272:.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:314:    'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166274:.opencode/skills/system-spec-kit/mcp_server/lib/enrichment/passive-enrichment.ts:129:      return ['[session] Context quality is CRITICAL. Consider running `memory_context({ mode: "resume" })` or `session_health` to diagnose.'];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166291:.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:89:describe('memory_context advisory metadata', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166306:.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:8:// Phase 020: Integrated into memory_context handler for query-intent
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166312:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:127:  it('returns null for memory_context (prevents recursive surfacing)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166313:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:128:    const result = await autoSurfaceAtToolDispatch('memory_context', { input: 'some context' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166314:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:132:  it('returns null for memory_search', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166315:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:133:    const result = await autoSurfaceAtToolDispatch('memory_search', { query: 'some query' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166316:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:137:  it('returns null for memory_match_triggers', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166317:.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:138:    const result = await autoSurfaceAtToolDispatch('memory_match_triggers', { prompt: 'some prompt' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166397:.opencode/skills/system-spec-kit/mcp_server/tests/session-manager-extended.vitest.ts:626:      expect(md).toContain('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166444:.opencode/skills/system-spec-kit/mcp_server/tests/memory-tools.vitest.ts:12:    content: [{ type: 'text', text: JSON.stringify({ data: { results: [], count: 0 }, meta: { tool: 'memory_search' } }) }],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166445:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:32:  handle_memory_context,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166446:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:238:   T021-T030: handle_memory_context MAIN HANDLER TESTS
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166447:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:242:  it('T021: handle_memory_context is a function', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166448:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:289:  it('T029: handleMemoryContext is alias for handle_memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166449:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:290:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166450:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:847:  it('T101: handle_memory_context is exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166451:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:868:  it('T105: handleMemoryContext is same as handle_memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166452:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:869:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166453:.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:902:      meta: { tool: 'memory_search' }
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166462:.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:123:describe('memory_search UX hook integration', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:166474:.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:304:  `).run(1, 'sess-1', 1, 0.9, now, later, 2, 1, 1, 'memory_search', 'call-1', 'rule-1', 0);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168179:/bin/zsh -lc "rg -n \"memory_match_triggers|memory_search|memory_context|session_bootstrap|session_resume|memory_save|memory_index_scan|memory_validate|memory_quick_search\" .opencode/skills/system-spec-kit/mcp_server/context-server.ts | sed -n '1,240p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168184:759:    'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168185:760:    'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168187:772:        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168191:882:    if (name === 'memory_context' && args.mode === 'resume') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168192:912:      name === 'memory_context' && args.mode === 'resume';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168193:964:    if (name !== 'memory_search' && name !== 'memory_context' && name !== 'memory_quick_search' && name !== 'session_health') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168194:977:    if ((name === 'memory_search' || name === 'memory_context') && result && !result.isError && result.content?.[0]?.text) {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168237:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:772:        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168242:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:882:    if (name === 'memory_context' && args.mode === 'resume') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168243:.opencode/skills/system-spec-kit/mcp_server/context-server.ts:912:      name === 'memory_context' && args.mode === 'resume';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168325:.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1263:      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168420:.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:433:      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168446:.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:123:    nextActions.add('Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` if you need a deeper state refresh.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168706:  1231	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168758:   433	      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168787:   462	  // ── Sub-call 3: CocoIndex availability (F046/F051: shared helper) ──
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168788:   463	  const cocoIndex: CocoIndexStatus = {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168789:   464	    available: isCocoIndexAvailable(),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:168793:   468	    hints.push('CocoIndex not installed. Install: `bash .opencode/skills/mcp-coco-index/scripts/install.sh`');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169672:   759	    'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169673:   760	    'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169685:   772	        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169830:- What did not work: CocoIndex was not usable in this run and returned cancelled calls, so I fell back to `rg` plus direct reads; the exact strict validator command still reports `cannot create temp file for here document: Operation not permitted` even though it ends with `RESULT: PASSED`; the phase folder still lacks the Level 3 spec docs the prompt expects, so this remained read-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169840:You are a research specialist in persistent memory architectures for AI agents, MCP server design, SQLite/FTS5 search systems, and agent-agnostic tool surfaces. Work like a systems analyst who can trace Go implementation details, separate durable patterns from packaging noise, and turn Engram's design into concrete improvements for `Code_Environment/Public`. Keep the analysis grounded in actual repository evidence, especially around tool profiles, session lifecycle, topic-key stability, passive capture, and search behavior.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169867:`Code_Environment/Public` already has Spec Kit Memory with semantic retrieval via `memory_search`, session continuity via `memory_context`, trigger-based recall via `memory_match_triggers`, causal links, health/status tooling, and context save flows through `generate-context.js`. It also has CocoIndex for semantic code search and code-graph tooling for structural queries. What it does **not** currently have is a first-class session lifecycle API comparable to `mem_session_start` / `mem_session_end`, nor a lightweight MCP tool-profile split equivalent to Engram's `ProfileAgent` versus `ProfileAdmin`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169887:11. Use CocoIndex plus grep to trace implementations and references. If CocoIndex is weak on Go files or times out, fall back to targeted grep plus direct file reads and state that fallback explicitly in the research notes.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169888:12. Compare Engram directly against Public's current memory stack: Spec Kit Memory, `memory_context`, `memory_search`, `memory_match_triggers`, `generate-context.js`, CocoIndex, and any relevant code-graph/session-recovery surfaces. Keep the comparison concrete rather than generic.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169959:- If CocoIndex does not index the Go repo well enough, use grep plus direct file reads and state the fallback explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:169993:- explicit comparison against current Public memory capabilities, especially Spec Kit Memory and CocoIndex
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170075:- What did not work: CocoIndex cancelled again on both the Go subtree and the Public handlers, so this pass relied on `rg` plus direct reads; the exact strict validator command ended with `RESULT: PASSED` but still emitted `cannot create temp file for here document: Operation not permitted`; the phase folder still appears to be missing the requested Level 3 spec docs, so this iteration stayed read-only and report-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170156:- What did not work: CocoIndex cancelled again on both the Go subtree and the Public handlers, so this pass relied on `rg` plus direct reads; the exact strict validator command ended with `RESULT: PASSED` but still emitted `cannot create temp file for here document: Operation not permitted`; the phase folder still appears to be missing the requested Level 3 spec docs, so this iteration stayed read-only and report-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170207:- What did not work: CocoIndex cancelled again on both the Go subtree and the Public handlers, so this pass relied on `rg` plus direct reads; the exact strict validator command ended with `RESULT: PASSED` but still emitted `cannot create temp file for here document: Operation not permitted`; the phase folder still appears to be missing the requested Level 3 spec docs, so this iteration stayed read-only and report-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170217:You are a research specialist in persistent memory architectures for AI agents, MCP server design, SQLite/FTS5 search systems, and agent-agnostic tool surfaces. Work like a systems analyst who can trace Go implementation details, separate durable patterns from packaging noise, and turn Engram's design into concrete improvements for `Code_Environment/Public`. Keep the analysis grounded in actual repository evidence, especially around tool profiles, session lifecycle, topic-key stability, passive capture, and search behavior.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170244:`Code_Environment/Public` already has Spec Kit Memory with semantic retrieval via `memory_search`, session continuity via `memory_context`, trigger-based recall via `memory_match_triggers`, causal links, health/status tooling, and context save flows through `generate-context.js`. It also has CocoIndex for semantic code search and code-graph tooling for structural queries. What it does **not** currently have is a first-class session lifecycle API comparable to `mem_session_start` / `mem_session_end`, nor a lightweight MCP tool-profile split equivalent to Engram's `ProfileAgent` versus `ProfileAdmin`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170264:11. Use CocoIndex plus grep to trace implementations and references. If CocoIndex is weak on Go files or times out, fall back to targeted grep plus direct file reads and state that fallback explicitly in the research notes.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170265:12. Compare Engram directly against Public's current memory stack: Spec Kit Memory, `memory_context`, `memory_search`, `memory_match_triggers`, `generate-context.js`, CocoIndex, and any relevant code-graph/session-recovery surfaces. Keep the comparison concrete rather than generic.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170336:- If CocoIndex does not index the Go repo well enough, use grep plus direct file reads and state the fallback explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170370:- explicit comparison against current Public memory capabilities, especially Spec Kit Memory and CocoIndex
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170472:  - Semantic/concept search → `mcp__cocoindex_code__search` (CocoIndex). Skill: `.opencode/skills/mcp-coco-index/`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170486:| **Research/exploration**  | `memory_match_triggers()` → `memory_context()` (unified) OR `memory_search()` (targeted) → Document findings                       |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170487:| **Code search**           | Semantic/concept → `CocoIndex search` · Structural (callers/imports/deps) → `code_graph_query` · Exact text → `Grep` · File paths → `Glob` · Read contents → `Read` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170488:| **Resume prior work**     | `/spec_kit:resume` OR `memory_context({ input: "resume previous work continue session", mode: "resume", profile: "resume", specFolder })` → Review checklist → Continue |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170512:1. **FIRST ACTION** — call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170543:**⚠️ BEFORE using ANY tool (except Gate Actions: memory_match_triggers, skill_advisor.py), you MUST pass all applicable gates below.**
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170549:1. Call `memory_match_triggers(prompt)` → Surface relevant context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170746:- What did not work: CocoIndex was not usable in this run and returned cancelled calls, so I fell back to `rg` plus direct reads; the exact strict validator command still reports `cannot create temp file for here document: Operation not permitted` even though it ends with `RESULT: PASSED`; the phase folder still lacks the Level 3 spec docs the prompt expects, so this remained read-only.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170756:You are a research specialist in persistent memory architectures for AI agents, MCP server design, SQLite/FTS5 search systems, and agent-agnostic tool surfaces. Work like a systems analyst who can trace Go implementation details, separate durable patterns from packaging noise, and turn Engram's design into concrete improvements for `Code_Environment/Public`. Keep the analysis grounded in actual repository evidence, especially around tool profiles, session lifecycle, topic-key stability, passive capture, and search behavior.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170783:`Code_Environment/Public` already has Spec Kit Memory with semantic retrieval via `memory_search`, session continuity via `memory_context`, trigger-based recall via `memory_match_triggers`, causal links, health/status tooling, and context save flows through `generate-context.js`. It also has CocoIndex for semantic code search and code-graph tooling for structural queries. What it does **not** currently have is a first-class session lifecycle API comparable to `mem_session_start` / `mem_session_end`, nor a lightweight MCP tool-profile split equivalent to Engram's `ProfileAgent` versus `ProfileAdmin`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170803:11. Use CocoIndex plus grep to trace implementations and references. If CocoIndex is weak on Go files or times out, fall back to targeted grep plus direct file reads and state that fallback explicitly in the research notes.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170804:12. Compare Engram directly against Public's current memory stack: Spec Kit Memory, `memory_context`, `memory_search`, `memory_match_triggers`, `generate-context.js`, CocoIndex, and any relevant code-graph/session-recovery surfaces. Keep the comparison concrete rather than generic.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170875:- If CocoIndex does not index the Go repo well enough, use grep plus direct file reads and state the fallback explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170909:- explicit comparison against current Public memory capabilities, especially Spec Kit Memory and CocoIndex
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170960:The prior iteration notes confirm two useful constraints for this pass: CocoIndex was flaky on the Go subtree, and the strongest unanswered work is now prioritization rather than basic discovery. I’m pulling the current iteration corpus and the exact implementation lines behind the likely roadmap candidates so the ranking stays source-backed instead of just opinionated.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:170989:allowed-tools: [Read, Write, Edit, Bash, Grep, Glob, Task, WebFetch, memory_context, memory_search]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171212:description: "Semantic code search via vector embeddings. CocoIndex Code enables natural-language discovery of relevant code, patterns, and implementations. CLI for direct use; MCP exposes a single `search` tool for AI agent integration."
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171219:# CocoIndex Code - Semantic Code Search via Vector Embeddings
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171221:Natural language code search through two complementary approaches: CLI (ccc) for speed and one-off queries, MCP server (1 tool: `search`) for AI agent integration via stdio transport.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171234:- User mentions "semantic search", "code search", "find similar code"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171247:- "find similar", "code search", "search codebase"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171396:CocoIndex Code provides two access patterns for semantic code search:
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171401:### CLI Approach (Primary) - CocoIndex Code CLI
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171438:- **What it does**: Engram persists session rows explicitly and exposes start/end as first-class tools. Public already has richer session orchestration through trusted session IDs, `memory_context`, `session_resume`, and `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171482:- What did not work: CocoIndex cancelled again on the Go subtree, so this iteration relied on `rg` plus direct reads; the exact strict validator command still emitted `cannot create temp file for here document: Operation not permitted`, but it finished with `RESULT: PASSED`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171492:You are a research specialist in persistent memory architectures for AI agents, MCP server design, SQLite/FTS5 search systems, and agent-agnostic tool surfaces. Work like a systems analyst who can trace Go implementation details, separate durable patterns from packaging noise, and turn Engram's design into concrete improvements for `Code_Environment/Public`. Keep the analysis grounded in actual repository evidence, especially around tool profiles, session lifecycle, topic-key stability, passive capture, and search behavior.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171519:`Code_Environment/Public` already has Spec Kit Memory with semantic retrieval via `memory_search`, session continuity via `memory_context`, trigger-based recall via `memory_match_triggers`, causal links, health/status tooling, and context save flows through `generate-context.js`. It also has CocoIndex for semantic code search and code-graph tooling for structural queries. What it does **not** currently have is a first-class session lifecycle API comparable to `mem_session_start` / `mem_session_end`, nor a lightweight MCP tool-profile split equivalent to Engram's `ProfileAgent` versus `ProfileAdmin`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171539:11. Use CocoIndex plus grep to trace implementations and references. If CocoIndex is weak on Go files or times out, fall back to targeted grep plus direct file reads and state that fallback explicitly in the research notes.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171540:12. Compare Engram directly against Public's current memory stack: Spec Kit Memory, `memory_context`, `memory_search`, `memory_match_triggers`, `generate-context.js`, CocoIndex, and any relevant code-graph/session-recovery surfaces. Keep the comparison concrete rather than generic.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171611:- If CocoIndex does not index the Go repo well enough, use grep plus direct file reads and state the fallback explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:171645:- explicit comparison against current Public memory capabilities, especially Spec Kit Memory and CocoIndex
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172154:/bin/zsh -lc 'rg -n "memory_context|memory_search|memory_match_triggers|generate-context|session_bootstrap|session_resume|CreateSession|sessionId|thread_key|topic_key|passive|provenance|sharedSpace|tenantId|governed" /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/dist/memory/generate-context.js' in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172180:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/context-server.ts:759:    'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172181:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/context-server.ts:760:    'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172183:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/context-server.ts:772:        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172187:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/context-server.ts:882:    if (name === 'memory_context' && args.mode === 'resume') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172188:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/context-server.ts:912:      name === 'memory_context' && args.mode === 'resume';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172189:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/context-server.ts:964:    if (name !== 'memory_search' && name !== 'memory_context' && name !== 'memory_quick_search' && name !== 'session_health') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172190:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/context-server.ts:977:    if ((name === 'memory_search' || name === 'memory_context') && result && !result.isError && result.content?.[0]?.text) {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172197:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:229:| `SPECKIT_PRESSURE_POLICY` | `true` | boolean | Token-pressure policy for memory_context responses. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172198:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:230:| `SPECKIT_AUTO_RESUME` | `true` | boolean | Automatic session resume context injection for memory_context. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172203:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/shared-memory.ts:250:  // memory_context/memory_match_triggers cannot be wired here yet.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172231:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:7:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172235:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:150:    console.warn('[memory_match_triggers] Failed to fetch memory records:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172236:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:184:/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172237:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:197:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172241:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:218:      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172242:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:220:        tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172243:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:225:          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172247:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:284:      console.warn('[memory_match_triggers] Decay failed:', message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172252:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:325:      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172253:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:336:      tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172256:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:374:        console.warn(`[memory_match_triggers] Failed to activate memory ${match.memoryId}:`, message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172257:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:390:          console.warn(`[memory_match_triggers] Co-activation failed for ${memoryId}:`, message);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172260:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:491:    console.warn(`[memory_match_triggers] Latency ${latencyMs}ms exceeds 100ms target`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172262:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:511:    tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172264:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:562:const handle_memory_match_triggers = handleMemoryMatchTriggers;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172265:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:565:  handle_memory_match_triggers,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172303:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:433:      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172313:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:222:export const handle_memory_search = lazyFunction(getMemorySearchModule, 'handle_memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172314:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:226:export const handle_memory_match_triggers = lazyFunction(getMemoryTriggersModule, 'handle_memory_match_triggers');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172315:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:320:export const handle_memory_context = lazyFunction(getMemoryContextModule, 'handle_memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172322:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:123:    nextActions.add('Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` if you need a deeper state refresh.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172337:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:60:// Feature catalog: Unified context retrieval (memory_context)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172341:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:87:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172345:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:124:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172348:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:386:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172349:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:397:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172364:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1078:/** Handle memory_context tool — L1 orchestration layer that routes to optimal retrieval strategy.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172365:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1092:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172366:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1117:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172367:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1231:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172370:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1250:  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172374:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1318:  // Phase C: Intent-to-profile auto-routing for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172376:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1375:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172377:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1393:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172378:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1471:    tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172379:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1478:      `For more granular control, use L2 tools: memory_search, memory_match_triggers`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172380:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1583:      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172381:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1584:      error: 'memory_context failed due to an internal error',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172382:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1606:const handle_memory_context = handleMemoryContext;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172383:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1609:  handle_memory_context,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172386:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/session-health.ts:128:    hints.push('No tool calls in >60 min. Consider calling `memory_context` to refresh session state.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172389:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts:90: * reliable retrieval via the `memory_match_triggers` tool. The scoring
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172406:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:42:  name: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172407:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:44:  inputSchema: { type: 'object', additionalProperties: false, properties: { input: { type: 'string', minLength: 1, description: 'The query, prompt, or context description (required)' }, mode: { type: 'string', enum: ['auto', 'quick', 'deep', 'focused', 'resume'], default: 'auto', description: 'Context retrieval mode: auto (detect intent), quick (fast triggers), deep (comprehensive search), focused (intent-optimized), resume (session recovery)' }, intent: { type: 'string', enum: ['add_feature', 'fix_bug', 'refactor', 'security_audit', 'understand', 'find_spec', 'find_decision'], description: 'Explicit task intent. If not provided and mode=auto, intent is auto-detected from input.' }, specFolder: { type: 'string', description: 'Limit context to specific spec folder' }, tenantId: { type: 'string', description: 'Tenant boundary for governed retrieval when memory_context routes to memory_search.' }, userId: { type: 'string', description: 'User boundary for governed retrieval when memory_context routes to memory_search.' }, agentId: { type: 'string', description: 'Agent boundary for governed retrieval when memory_context routes to memory_search.' }, sharedSpaceId: { type: 'string', description: 'Shared-space boundary for governed retrieval when memory_context routes to memory_search.' }, limit: { type: 'number', minimum: 1, maximum: 100, description: 'Maximum results (mode-specific defaults apply)' }, sessionId: { type: 'string', description: 'Optional server-issued session identifier for working-memory continuity. When provided, it must match an existing server-managed session or the call is rejected. Omit it to let the server generate a new session for this request.' }, enableDedup: { type: 'boolean', default: true, description: 'Enable session deduplication' }, includeContent: { type: 'boolean', default: false, description: 'Include full file content in results' }, includeTrace: { type: 'boolean', default: false, description: 'Include provenance-rich trace data (scores, source, trace) in results when underlying memory_search is called' }, tokenUsage: { type: 'number', minimum: 0.0, maximum: 1.0, description: "Optional caller token usage ratio (0.0-1.0)" }, anchors: { type: 'array', items: { type: 'string' }, description: 'Filter content to specific anchors (e.g., ["state", "next-steps"] for resume mode)' }, profile: { type: 'string', enum: ['quick', 'research', 'resume', 'debug'], description: 'Optional response profile formatter. Returns a reduced or mode-aware response shape when profile formatting is enabled.' } }, required: ['input'] },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172408:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:49:  name: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172416:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:190:// E3: Simplified search — 3 params, sensible defaults, delegates to memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172417:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:193:  description: '[L2:Core] Simplified search — query + optional limit + optional spec folder. Delegates to memory_search with sensible defaults (intent auto-detect ON, dedup ON, content included, limit 10). Use this when you want fast search without configuring 31 parameters.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172422:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:211:  name: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172445:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:741:  description: '[L1:Orchestration] Resume session with combined memory, code graph, and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. For the canonical first-call recovery path on session start or after /clear, prefer session_bootstrap. Use minimal: true to skip the heavy memory context call and return code graph, CocoIndex, structural context, hints, and session-quality metadata without the full memory payload.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172459:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:100:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172465:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:340:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172474:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:482:/** Handle memory_search tool — performs hybrid vector/BM25 search with intent-aware ranking.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172482:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:554:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172483:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:566:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172484:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:594:          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172485:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:613:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172486:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:625:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172491:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:751:  const cacheKey = toolCache.generateCacheKey('memory_search', cacheArgs);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172499:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1044:      toolCache.set(cacheKey, cachePayload, { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172512:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1374:const handle_memory_search = handleMemorySearch;
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172513:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1377:  handle_memory_search,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172515:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:426:- `memory_context` (unified context retrieval)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172516:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:427:- `memory_search` (semantic search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172517:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:428:- `memory_match_triggers` (fast trigger matching)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172520:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:465:- [ ] `memory_search()` returns results (or empty if no memories are indexed yet)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172521:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:530:### memory_context: Unified Context Retrieval
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172522:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:532:`memory_context()` is the primary entry point for context loading. It detects task intent and routes to the optimal retrieval strategy automatically.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172523:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:548:### memory_search: Semantic Search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172524:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:550:`memory_search()` runs vector-based similarity search across all indexed memories.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172525:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:559:### memory_match_triggers: Fast Keyword Lookup
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172526:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:561:`memory_match_triggers()` provides sub-50ms keyword-based matching. Use it for immediate context surfacing at the start of a conversation.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172528:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:629:- `ContextEnvelope`: Wraps all `memory_context()` responses with metadata (mode used, memories returned, intent detected)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172529:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:681:**Behind the scenes:** The AI calls `memory_context()` with `mode: "resume"` and `anchors: ["state", "next-steps"]`, then returns the previous session state.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172530:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:692:1. AI calls `memory_context({ input: "add user profiles", mode: "auto" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172531:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1047:MCP TOOLS: memory_context, memory_search, memory_match_triggers,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172532:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1064:| v1.7.x | 2026-02-20 | Cross-encoder reranking enabled by default. Co-activation score boost fix. Query expansion on deep mode. Evidence gap warnings. MMR reranking with intent-mapped lambda. Phase system support (recursive validation, phase detection scoring). Feature flag updates. `memory_context` tokenUsage parameter. 28-tool surface area. |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172534:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:416:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172536:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:709:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172580:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:9:  - "memory_context"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172581:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:10:  - "memory_search"
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172582:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:200:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172584:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:547:**Query routing:** Structural queries (callers, imports, dependencies) go to `code_graph_query`. Semantic and concept queries go to CocoIndex (`mcp__cocoindex_code__search`). Session and memory queries go to `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172585:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:557:**Start here for most tasks**: `memory_context` (L1) automatically figures out what you need. Use the lower-level tools when you want precise control.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172586:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:563:##### `memory_context`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172592:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:587:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172594:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:601:Resume session with combined memory, code graph and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. The response carries freshness-aware code-graph status (`fresh`, `stale`, `empty`, `error`) instead of count-only health. For the canonical first-call recovery path on session start or after `/clear`, prefer `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172597:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:622:##### `memory_search`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172600:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:646:  "tool": "memory_search",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172603:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:674:##### `memory_match_triggers`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172604:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:688:  "tool": "memory_match_triggers",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172616:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:1326:  "tool": "memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172622:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:1538:| Find a past decision | `memory_context` | Set `intent: "find_decision"` |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172623:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:1539:| Search for specific terms | `memory_search` | Use `concepts: ["term1", "term2"]` for AND search |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172624:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:1540:| Check triggers on every prompt | `memory_match_triggers` | Pass the user's prompt text |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172625:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:1556:**What you see**: Irrelevant or low-scoring results from `memory_search` or `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172626:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:1567:{ "tool": "memory_search", "arguments": { "query": "your query", "min_quality_score": 0.5 } }
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172627:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/README.md:1717:Start with `memory_context` for all retrieval tasks. It handles intent detection and routing automatically. Use `memory_search` when you want explicit control over channels. Use `memory_match_triggers` when processing a raw prompt at the start of each turn. Use L4-L7 tools only for mutation, analysis or maintenance.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172632:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:4:// Dispatch for L1 Orchestration tool: memory_context (T303).
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172633:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:11:export const TOOL_NAMES = new Set(['memory_context']);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172634:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:16:    case 'memory_context': return handleMemoryContext(parseArgs<ContextArgs>(validateToolArgs('memory_context', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172645:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:62:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172646:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:64:  'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172647:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:78:    case 'memory_search':         return handleMemorySearch(parseArgs<SearchArgs>(validateToolArgs('memory_search', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172648:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:80:      // E3: Delegate to memory_search with sensible defaults
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172651:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:99:    case 'memory_match_triggers': return handleMemoryMatchTriggers(parseArgs<TriggerArgs>(validateToolArgs('memory_match_triggers', args)));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172695:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:112:  includeTrace: z.boolean().optional(), // CHK-040: Forward to internal memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172721:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:397:  memory_context: memoryContextSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172722:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:398:  memory_search: memorySearchSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172723:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:400:  memory_match_triggers: memoryMatchTriggersSchema as unknown as ToolInputSchema,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172729:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:462:  memory_context: ['input', 'mode', 'intent', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'sessionId', 'enableDedup', 'includeContent', 'includeTrace', 'tokenUsage', 'anchors', 'profile'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172730:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:463:  memory_search: ['cursor', 'query', 'concepts', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'sessionId', 'enableDedup', 'tier', 'contextType', 'useDecay', 'includeContiguity', 'includeConstitutional', 'enableSessionBoost', 'enableCausalBoost', 'includeContent', 'anchors', 'min_quality_score', 'minQualityScore', 'bypassCache', 'rerank', 'applyLengthPenalty', 'applyStateLimits', 'minState', 'intent', 'autoDetectIntent', 'trackAccess', 'includeArchived', 'mode', 'includeTrace', 'profile'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172732:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:465:  memory_match_triggers: ['prompt', 'specFolder', 'tenantId', 'userId', 'agentId', 'sharedSpaceId', 'limit', 'session_id', 'turnNumber', 'include_cognitive'],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172752:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/README.md:27:- `context-tools.ts` - dispatch for `memory_context`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172753:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tools/README.md:40:- `memory-tools.ts` implements the `memory_quick_search` delegation path by building a richer `memory_search` request and relabeling the returned envelope metadata back to `memory_quick_search`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172883:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1263:      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172884:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1264:      : 'memory_search({ query: "last session" })';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172895:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/README.md:93:1. User queries memory_search
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172913:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:384:  it('C13: Response meta.tool is memory_search', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172914:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:388:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172979:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts:224:  //   recovery (0.20)      — A memory_context({ mode: "resume" }) call is the most
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172980:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:83:      validateToolInputSchema('memory_context', {}, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172981:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:119:      validateToolInputSchema('memory_context', { input: 'resume', mode: 'invalid-mode' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172982:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:133:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172983:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:137:    expect(errorSpy.mock.calls.some((call) => String(call[0]).includes('[schema-validation] memory_search:'))).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172984:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:240:   4. memory_search LIMIT CONTRACT (schema + runtime alignment)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172985:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:243:describe('memory_search limit contract', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172986:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:246:      validateToolInputSchema('memory_search', { cursor: 'opaque-cursor-token' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172987:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:252:      validateToolArgs('memory_search', { cursor: 'opaque-cursor-token' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172988:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:258:      validateToolInputSchema('memory_search', { concepts: ['alpha', 'beta'] }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172989:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:264:      validateToolInputSchema('memory_search', {}, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172990:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:270:      validateToolArgs('memory_search', { query: 'ab', limit: 100 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172991:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:276:      validateToolArgs('memory_search', { query: 'ab', limit: 101 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172992:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:282:      validateToolInputSchema('memory_search', { query: 'ab', limit: 101 }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172993:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:288:      validateToolArgs('memory_search', { concepts: ['solo'] });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172994:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:292:  it('public schema rejects unknown memory_search parameters', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172995:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:294:      validateToolInputSchema('memory_search', { query: 'valid query', unexpected: true }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172996:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:300:      validateToolInputSchema('memory_search', { query: 'a' }, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172997:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:304:  it('runtime rejects unknown memory_search parameters', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172998:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:306:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:172999:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:310:  it('runtime accepts governed scope fields for memory_search', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173000:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:312:      validateToolArgs('memory_search', {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173003:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:322:  it('public and runtime schemas accept response profiles for memory_search', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173004:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:329:      validateToolInputSchema('memory_search', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173005:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:331:    expect(validateToolArgs('memory_search', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173007:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:336:  it('public and runtime schemas accept governed scope fields for memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173010:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:346:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173011:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:348:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173012:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:351:  it('public and runtime schemas accept response profiles for memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173013:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:358:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173014:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:360:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173018:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:378:  it('public and runtime schemas accept governed scope fields for memory_match_triggers', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173021:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:389:      validateToolInputSchema('memory_match_triggers', args, TOOL_DEFINITIONS);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173022:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:391:    expect(validateToolArgs('memory_match_triggers', args)).toEqual(args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173166:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:59:    it('T516-2: handle_memory_search alias is exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173167:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:60:      expect(typeof handler.handle_memory_search).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173175:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:86:  'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173176:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:87:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173177:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:89:  'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173186:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:460:    recommendedCalls.push('memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173187:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:463:    recommendedCalls.push('memory_match_triggers({ prompt: "<your task>" })');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173188:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:482:      graphRetrieval: 'For broad topic questions, use memory_search with retrievalLevel: "global" for community-level results. For specific memories, use "local" (default). Use "auto" for automatic fallback.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173287:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:23:      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173291:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/README.md:70:- `MEMORY_AWARE_TOOLS` currently includes `memory_context`, `memory_search`, `memory_match_triggers`, `memory_list`, `memory_save`, and `memory_index_scan`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173294:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:482:describe('T059: autoDetectIntent Parameter (memory_search)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173299:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:50:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173301:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:61:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173305:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:77:      content: 'Context was compacted and auto-recovered from the cached compact brief. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173308:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:140:        '- `memory_context({ input, mode })` — unified context retrieval',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173309:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:141:        '- `memory_match_triggers({ prompt })` — fast trigger matching',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173310:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:142:        '- `memory_search({ query })` — semantic search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173313:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:185:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173314:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:190:      content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173315:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:202:      content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173436:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/claude/README.md:31:Hooks are transport reliability, not separate business logic. They call the same retrieval primitives (`memory_match_triggers`, `memory_context`) that other runtimes call explicitly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173465:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:977:  // Including it here caused all candidates to be filtered out when memory_context
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173531:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:181:  it('T022: memory_search has tool-specific hints', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173532:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:182:    expect(TOOL_SPECIFIC_HINTS.memory_search).toBeDefined();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173533:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:183:    expect(typeof TOOL_SPECIFIC_HINTS.memory_search).toBe('object');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173534:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:221:  it('T029: memory_search EMBEDDING_FAILED has contextual hint', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173535:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:224:      TOOL_SPECIFIC_HINTS.memory_search?.[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173536:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:244:    const searchHint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173537:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:246:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173538:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:301:      'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173539:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:315:    const hasSearch = hasSpecificHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173540:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:356:    const searchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173541:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:362:    const searchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173542:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:365:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173543:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:669:  it('T087: QUERY_TOO_LONG suggests memory_match_triggers()', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173544:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:672:      a.includes('memory_match_triggers()')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173545:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:713:    const toolSpecific = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173546:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:718:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED]
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173547:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:725:    const allSearchHints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173574:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:82:      const key1 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173575:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:83:      const key2 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173576:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:88:      const key1 = generateCacheKey('memory_search', { query: 'auth' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173577:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:89:      const key2 = generateCacheKey('memory_search', { query: 'login' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173578:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:95:      const key1 = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173579:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:352:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173580:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:353:      const key2 = generateCacheKey('memory_search', { query: 'test2' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173581:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:355:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173582:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:356:      set(key2, 'value2', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173583:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:358:      const invalidated = invalidateByTool('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173584:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:366:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173585:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:369:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173586:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:380:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173587:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:383:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173588:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:394:      const searchKey = generateCacheKey('memory_search', { query: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173589:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:395:      const triggerKey = generateCacheKey('memory_match_triggers', { prompt: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173590:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:396:      set(searchKey, 'search_result', { toolName: 'memory_search' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173591:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:397:      set(triggerKey, 'trigger_result', { toolName: 'memory_match_triggers' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173592:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:423:      const key = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173593:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:427:        'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173594:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:436:      expect(invalidateByTool('memory_search')).toBe(0);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173595:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:439:      const second = withCache('memory_search', args, async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173596:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:589:      const key = generateCacheKey('memory_search', args);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173597:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:593:        'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173598:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:603:      const second = withCache('memory_search', args, async () => 'fresh-after-shutdown');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173599:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34:The `pipeline/` directory implements the core retrieval pipeline behind `memory_search`. Each search request flows through four sequential stages, each with a defined I/O contract and clear responsibility boundary. The pipeline supports hybrid, vector and multi-concept search types with optional deep-mode query expansion, cross-encoder reranking, MMR diversity pruning and MPAB chunk-to-parent reassembly.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173626:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:76:    it('T517-2: handle_memory_match_triggers alias exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173627:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:77:      expect(typeof handler.handle_memory_match_triggers).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173631:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:42:    toolPattern: /^(read|memory_context|memory_search|memory_list)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173632:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:49:    toolPattern: /^(grep|memory_search)$/i,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173676:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:6:  { tool: 'memory_context', handler: 'handleMemoryContext', layer: 'L1' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173677:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:7:  { tool: 'memory_search', handler: 'handleMemorySearch', layer: 'L2' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173678:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:8:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers', layer: 'L2' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173679:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:33:  { camel: 'handleMemorySearch', snake: 'handle_memory_search' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173680:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:34:  { camel: 'handleMemoryMatchTriggers', snake: 'handle_memory_match_triggers' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173681:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:56:  { camel: 'handleMemoryContext', snake: 'handle_memory_context' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173694:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:51:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173695:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:62:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173696:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:73:      content: 'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173697:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:106:        '- `memory_context({ input, mode })` - unified context retrieval',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173698:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:107:        '- `memory_match_triggers({ prompt })` - fast trigger matching',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173699:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:108:        '- `memory_search({ query })` - semantic search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173702:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:149:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173703:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:155:    content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173704:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:163:    content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173710:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:89:describe('memory_context advisory metadata', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173753:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/compact-inject.ts:63:    'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173756:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:4:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173770:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:175:Packet `026-graph-and-context-optimization/010-fts-capability-cascade-floor` freezes the lexical capability contract that packet `002-implement-cache-warning-hooks` now consumes. `memory_search` responses expose:
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173774:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:86:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173804:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:18:        memory_context: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173805:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:19:        memory_search: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173806:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:21:        memory_match_triggers: 3500,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173807:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/tiered-injection-turnNumber.vitest.ts:183:      expect(typeof handlerExports.handle_memory_match_triggers).toBe('function');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173813:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:1:// TEST: memory_context per-channel eval logging (T056)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173814:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:88:describe('T056: memory_context emits per-strategy channel eval rows', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173815:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:53:  memory_search: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173816:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:55:  memory_context: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173817:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:56:  memory_match_triggers: ERROR_CODES.SEARCH_FAILED,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173855:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:159:      'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173856:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:160:      'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173857:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:162:      'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173860:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:292:      'memory_context', 'memory_search', 'memory_quick_search', 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173864:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:927:        { id: 'call-1', params: { name: 'memory_search', arguments: {} } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173865:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:944:      expect(callArgs[0]).toBe('memory_search')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173866:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1054:              name: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173868:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1103:        memoryAwareTools: new Set<string>(['memory_search']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173869:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1113:        { id: 'call-5', params: { name: 'memory_search', arguments: { query: 'hook validation' } } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173870:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1123:    it('T000g: memory_context resume mode invokes TM-05 compaction hook at runtime', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173871:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1131:        memoryAwareTools: new Set<string>(['memory_context']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173872:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1144:          params: { name: 'memory_context', arguments: { input: 'session resume context', mode: 'resume' } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173873:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1157:    it('T000h: memory_context non-resume mode keeps SK-004 memory-aware path', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173874:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1164:        memoryAwareTools: new Set<string>(['memory_context']),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173875:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1177:          params: { name: 'memory_context', arguments: { input: 'focused retrieval context', mode: 'focused' } },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173876:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1563:      const response = errorsModule!.buildErrorResponse!('memory_search', testError, { query: 'test' })
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173877:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1581:      const hint = errorsModule!.getRecoveryHint!('memory_search', 'UNKNOWN_TOOL')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173878:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1614:    it('T28: L1 budget = 3500 (memory_context)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173879:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1619:      expect(layerDefs!.getTokenBudget!('memory_context')).toBe(3500)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173880:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1622:    it('T28b: L2 budget = 3500 (memory_search)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173881:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1627:      expect(layerDefs!.getTokenBudget!('memory_search')).toBe(3500)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173882:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1703:    const expectedAwareTools = ['memory_context', 'memory_search', 'memory_match_triggers', 'memory_list', 'memory_save', 'memory_index_scan']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173883:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2084:      'memory_context': '[L1:Orchestration]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173884:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2085:      'memory_search': '[L2:Core]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173885:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2086:      'memory_match_triggers': '[L2:Core]',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173886:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2131:    it('T000e: memory_context supports optional tokenUsage (0.0-1.0)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173887:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2132:      expect(toolSchemasCode).toMatch(/name:\s*'memory_context'[\s\S]*?tokenUsage:\s*\{\s*type:\s*'number'/)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173888:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2315:        'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173889:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2341:      expect(result).toContain('memory_context')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173890:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2342:      expect(result).toContain('memory_search')
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173891:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/review-fixes.vitest.ts:41:    const result = validateToolArgs('memory_search', {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173892:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:39:| Tool-Specific Hints | 6 tools | memory_search, checkpoint_restore, memory_save, memory_index_scan, memory_drift_why, memory_causal_link |
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173893:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:132:  return buildErrorResponse('memory_search', error, { query });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173894:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:142:const hint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173900:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:30:    tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173901:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:37:    tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173902:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:43:    tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173903:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:176:  { tool: 'memory_context', handler: 'handleMemoryContext' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173904:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:177:  { tool: 'memory_search', handler: 'handleMemorySearch' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173905:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:179:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173906:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:357:      'Use memory_match_triggers() for prompt-based matching instead'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173907:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:360:    toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173911:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:539:      'Check memory_search() for existing similar content'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173912:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:694:  memory_search: {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173913:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:700:        'Try memory_match_triggers() for trigger-based matching'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173914:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:703:      toolTip: 'memory_match_triggers()'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173923:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:117:        memory_context: 'L1',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173924:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:118:        memory_search: 'L2',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173925:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:120:        memory_match_triggers: 'L2',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173926:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:194:        { tool: 'memory_context', expected: '[L1:Orchestration]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173927:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:195:        { tool: 'memory_search', expected: '[L2:Core]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173928:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:221:      const result = mod.enhanceDescription('memory_context', 'Some description text');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173929:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:227:        { tool: 'memory_search', desc: 'Search memories', prefix: '[L2:Core]' },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173930:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:242:      expect(mod.enhanceDescription('memory_context', '')).toBe('[L1:Orchestration] ');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173931:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:252:        { tool: 'memory_context', expected: 3500 },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173932:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:253:        { tool: 'memory_search', expected: 3500 },
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173933:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:270:      expect(typeof mod.getTokenBudget('memory_context')).toBe('number');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173934:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:280:      const info = expectLayerInfo(mod.getLayerInfo('memory_context'));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173935:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:287:      expect(info.tools).toContain('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173936:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:291:      const info1 = mod.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173937:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:292:      const info2 = mod.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173938:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:301:      const info = expectLayerInfo(mod.getLayerInfo('memory_search'));
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173939:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:430:      const toolSamples = ['memory_context', 'memory_search', 'memory_list',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173947:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:20:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173948:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:58:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173949:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:97:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173950:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:108:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173951:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:135:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173952:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:143:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173953:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:152:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173954:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:186:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173955:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:206:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173956:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:254:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173957:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:312:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173958:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:352:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173959:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:363:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173960:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:373:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173961:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:384:        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173962:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:409:        tool: 'memory_search'
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173965:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:30:      "expectedResultDescription": "Should surface memories about adaptive-fusion.ts (7 intent profiles), intent-classifier.ts, and memory_context intent routing. Cross-document because the behavior spans multiple modules.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173966:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:85:      "query": "memory_context returns wrong results when token pressure is high",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173967:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:251:      "notes": "From T007b Pattern 3: feature description passed to memory_context before implementation."
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173968:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:415:      "query": "the memory_search tool returns stale results after index rebuild",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173969:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:425:      "query": "what is the difference between memory_context and memory_search for context retrieval",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173970:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:430:      "expectedResultDescription": "Should surface both memory_context (L1 unified entry) and memory_search (L2 core) tool schemas and any documentation comparing their use cases.",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173973:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:725:      "query": "when should I use memory_search versus memory_context",
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173977:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:250:  it('T020-02: Generates memory_search command with sessionId when specFolder is not provided', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:173978:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:254:  it('T020-03: Generates generic memory_search when neither specFolder nor sessionId is provided', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174017:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:127:  it('returns null for memory_context (prevents recursive surfacing)', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174018:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:128:    const result = await autoSurfaceAtToolDispatch('memory_context', { input: 'some context' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174019:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:132:  it('returns null for memory_search', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174020:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:133:    const result = await autoSurfaceAtToolDispatch('memory_search', { query: 'some query' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174021:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:137:  it('returns null for memory_match_triggers', async () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174022:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:138:    const result = await autoSurfaceAtToolDispatch('memory_match_triggers', { prompt: 'some prompt' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174023:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:52: * Token-pressure policy for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174024:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:60: * Automatic session resume context injection for memory_context.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174027:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:287:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174028:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:296:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174029:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:302:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174030:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:310:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174031:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:311:    expect(resp.meta.tool).toBe('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174032:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:318:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174033:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:328:  it('F7: Tool-specific hints included for memory_search + E001', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174034:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:330:    const resp = buildErrorResponse('memory_search', err);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174035:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:353:    const err = createErrorWithHint('E040', 'fail', {}, 'memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174036:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:469:  it('K2: Has memory_search, checkpoint_restore, memory_save', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174037:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:470:    expect('memory_search' in TOOL_SPECIFIC_HINTS).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174038:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:476:    const searchHints = TOOL_SPECIFIC_HINTS['memory_search'];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174039:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:492:  it('L1: Returns tool-specific hint for memory_search + E001', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174040:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:493:    const hint = getRecoveryHint('memory_search', 'E001');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174041:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:512:    const hint = getRecoveryHint('memory_search', 'E040');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174042:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:524:  it('M1: Returns true for known tool+code (memory_search, E001)', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174043:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:525:    expect(hasSpecificHint('memory_search', 'E001')).toBe(true);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174044:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:543:    const hints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174045:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:550:    const hints = getAvailableHints('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174046:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:48:  liveBaselineResolution: 'code_graph_query' | 'memory_context' | 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174047:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:143:    return 'memory_context_then_grep';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174048:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:146:  return 'memory_context';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174049:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:162:    if (resolution === 'memory_context_then_grep') {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174052:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:133:    expect(matchRule('memory_search', 'spec.md error context')).not.toBeNull();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174053:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:134:    expect(matchRule('memory_context', 'spec.md metadata')).not.toBeNull();
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174057:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:181:const key = generateCacheKey('memory_search', { query: 'test' });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174058:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:184:set(key, searchResults, { toolName: 'memory_search', ttlMs: 30000 });
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174059:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:196:  'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174060:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:210:// Automatically clears memory_search, memory_match_triggers, etc.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174075:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:4:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174076:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:312:    'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174077:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:313:    'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174078:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:314:    'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174083:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:1:// TEST: memory_search per-channel eval logging (T056)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174084:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:106:describe('T056: memory_search emits per-channel eval rows', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174085:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:223:    followUps.push(`Use memory_context with specFolder "${uniqueFolders[0]}" for full context`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174178:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/session-manager-extended.vitest.ts:626:      expect(md).toContain('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174199:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:123:describe('memory_search UX hook integration', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174203:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:32:  handle_memory_context,
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174204:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:238:   T021-T030: handle_memory_context MAIN HANDLER TESTS
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174205:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:242:  it('T021: handle_memory_context is a function', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174206:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:289:  it('T029: handleMemoryContext is alias for handle_memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174207:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:290:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174208:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:847:  it('T101: handle_memory_context is exported', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174209:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:868:  it('T105: handleMemoryContext is same as handle_memory_context', () => {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174210:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:869:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174211:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:902:      meta: { tool: 'memory_search' }
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174243:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:50:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174244:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:68:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174245:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:83:    const response = buildErrorResponse('memory_search', error);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174270:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:304:  `).run(1, 'sess-1', 1, 0.9, now, later, 2, 1, 1, 'memory_search', 'call-1', 'rule-1', 0);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174322:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-tools.vitest.ts:12:    content: [{ type: 'text', text: JSON.stringify({ data: { results: [], count: 0 }, meta: { tool: 'memory_search' } }) }],
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174408:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:50:    tools: ['memory_context', 'session_resume', 'session_bootstrap']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174409:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:59:    tools: ['memory_search', 'memory_quick_search', 'memory_save', 'memory_match_triggers']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174410:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:132:const budget = getTokenBudget('memory_search');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174411:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:139:const enhanced = enhanceDescription('memory_search', 'Search memories');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174498:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/enrichment/passive-enrichment.ts:129:      return ['[session] Context quality is CRITICAL. Consider running `memory_context({ mode: "resume" })` or `session_health` to diagnose.'];
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174506:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:8:// Phase 020: Integrated into memory_context handler for query-intent
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:174519:CocoIndex cancelled again on this workspace, so I’m following the fallback the research brief asked for: targeted `rg` plus direct source reads. I’m drilling into the exact Engram and Public sections that change the adoption ranking: profile-gated tools, topic-key upserts, explicit session lifecycle, passive capture, and project/scope hygiene.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176434:  1231	      tool: 'memory_context',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176453:  1250	  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176629:   433	      hints.push('Memory resume failed. Try memory_context manually.');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176658:   462	  // ── Sub-call 3: CocoIndex availability (F046/F051: shared helper) ──
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176659:   463	  const cocoIndex: CocoIndexStatus = {
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176660:   464	    available: isCocoIndexAvailable(),
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176664:   468	    hints.push('CocoIndex not installed. Install: `bash .opencode/skills/mcp-coco-index/scripts/install.sh`');
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176929:   218	      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176931:   220	        tool: 'memory_match_triggers',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176936:   225	          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176961:   759	    'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176962:   760	    'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:176974:   772	        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:177007:    50	    tools: ['memory_context', 'session_resume', 'session_bootstrap']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:177016:    59	    tools: ['memory_search', 'memory_quick_search', 'memory_save', 'memory_match_triggers']
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178188:   250	  // memory_context/memory_match_triggers cannot be wired here yet.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178291:482:/** Handle memory_search tool — performs hybrid vector/BM25 search with intent-aware ranking.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178444:   100	// Feature catalog: Semantic and lexical search (memory_search)
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178723:   482	/** Handle memory_search tool — performs hybrid vector/BM25 search with intent-aware ranking.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178795:   554	        tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178807:   566	      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178835:   594	          tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178854:   613	      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178866:   625	      tool: 'memory_search',
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:178992:   751	  const cacheKey = toolCache.generateCacheKey('memory_search', cacheArgs);
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179216:- What did not work: CocoIndex cancelled again on the Go and TypeScript searches in this run, so the pass fell back to `rg` plus direct source reads; this iteration also stayed read-only and did not attempt the phase-folder doc/update workflow.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179305:- What did not work: CocoIndex cancelled again on the Go and TypeScript searches in this run, so the pass fell back to `rg` plus direct source reads; this iteration also stayed read-only and did not attempt the phase-folder doc/update workflow.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179333:- **Why it matters for us**: Engram’s formatter is weaker overall, but more predictable. A cheap recent-session digest inside Public’s existing resume/bootstrap path would improve startup clarity without sacrificing graph/CocoIndex/status data.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179374:- **What it does**: Engram uses direct topic-key matches, `sanitizeFTS()`, and `fts.rank` over a single memory-oriented surface. Public already combines hybrid retrieval, scoped continuation, trigger hygiene, and explicit routing to CocoIndex and code graph tools.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179419:- What did not work: CocoIndex was blocked on this external tree, so the pass fell back to `rg` plus direct source reads; the phase folder also does not currently contain a canonical `research/research.md`, so this iteration stayed synthesis-only instead of phase-doc consolidation.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179446:- **Why it matters**: The strongest convergence is not on SQLite, markdown, vectors, or graphs. It is that agents need a taught operating protocol. For Spec Kit Memory, the next win is a thinner memory action card/profile over existing `memory_context`, `memory_search`, `memory_save`, `session_bootstrap`, and recovery flows.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179453:- **Why it matters**: Cross-system agreement is that one universal search endpoint should not also own repair, review, recovery, and governance. Public should keep `memory_search` narrow and continue growing explicit doctor/review/passive-capture lanes around it.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179467:- **Why it matters**: This is the most reusable Engram-specific idea. Public should keep prompt/session continuity outside `memory_search` and add a deterministic recent-session digest inside `session_bootstrap`/`session_resume`, while still avoiding a second explicit lifecycle authority.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179482:Turn the convergence into a four-track adoption matrix: `1)` thin startup/compaction memory action card, `2)` doctor/review/repair surfaces around existing retrieval, `3)` `thread_key` + exact lookup/timeline prototype, `4)` explicit non-goals: no second lifecycle authority, no scope replatforming, no collapse of code search into memory search.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179505:- **Migration steps**: 1. Extract the current “Key tools”, “Session Recovery”, “Structural Bootstrap”, and “Tool Routing” guidance from `context-server.ts` into the new helper. 2. Define one stable default profile grouping `memory_context`, `memory_search`, `memory_save`, `session_bootstrap`, `session_resume`, and a recovery grouping around `memory_health`, `session_health`, and `memory_index_scan`. 3. Keep `TOOL_DEFINITIONS` and dispatch unchanged so this remains presentation-only. 4. Extend `tests/context-server.vitest.ts` to assert the new formatted action card appears in startup instructions and that no tool count/registration behavior changes.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179514:- **Migration steps**: 1. Implement the digest helper as a pure formatter over the existing `memoryResult` and accepted cached-summary data. 2. In `session-resume.ts`, build the digest after `memoryResult` is loaded and before `payloadContract` is finalized, then append a stable section key. 3. In `session-bootstrap.ts`, pass the digest through to `nextActions`/summary text instead of adding a second fetch path. 4. Extend `tests/session-resume.vitest.ts` to assert digest presence/order and `tests/session-bootstrap.vitest.ts` to assert bootstrap reuses the digest. 5. Keep `resolveTrustedSession()` and the `memory_context` session-scope error path unchanged so the digest remains additive, not authoritative.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179518:### Finding 3: Add an explicit read-only doctor/review surface that orchestrates existing diagnostics, instead of widening `memory_search`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179520:- **What it does**: Engram keeps chronology, capture, and lifecycle-adjacent work in separate tools instead of overloading `mem_search`. Public already follows that direction structurally: `memory_search` adds progressive disclosure after retrieval, `memory_health` handles diagnostics, `session_health` handles readiness, and `passive-enrichment.ts` only adds non-durable hints.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179521:- **Why it matters**: The missing piece is a single read-only orchestration surface that says “what is wrong, which existing tool should I call next, and which actions are safe.” That strengthens retrieval hygiene without pushing repair flags, review logic, or passive capture into `memory_search`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179523:- **Migration steps**: 1. Ship `memory_doctor` as a read-only composite that calls existing `handleMemoryHealth()` and `handleSessionHealth()` and summarizes when to use `memory_index_scan`, `session_bootstrap`, or `code_graph_scan`. 2. Add a focused `mode: 'aliases'` path that reuses `memory_health(reportMode: 'divergent_aliases')` instead of duplicating alias logic. 3. Keep `memory_search` unchanged; do not add repair or review flags there. 4. Leave `lib/enrichment/passive-enrichment.ts` non-durable and explicitly treat governed passive capture as a later feature, not part of this adopt-now slice. 5. Add a new handler test file for `memory_doctor` and extend schema/dispatch tests so the composite surface is covered without weakening the current confirmation gates on mutating repair.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179695:- Fallback note: CocoIndex was unavailable for this external path in-session, so this pass used targeted grep plus direct file reads.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179725:- **What it does**: Public's `memory_search` is explicitly semantic-first, then runs a hybrid pipeline over vector, FTS, BM25, graph, and degree lanes with weighted RRF and default reranking. Within that fusion, vector stays primary, FTS is downweighted to `0.3` because higher weighting flooded top-k with noisy lexical matches, BM25 stays at `0.6` for breadth, and lexical-only fallback happens only after hybrid attempts fail. Engram has no semantic lane here; after exact `topic_key` lookup it relies on sanitized FTS5 `MATCH` plus `fts.rank`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179732:- **What it does**: Public already separates lexical behaviors. `memory_match_triggers` does exact trigger-phrase matching with binary scores, decay, activation, co-activation, and tiered content shaping. Learned feedback writes inferred aliases into a separate `learned_triggers` column with a 30-day TTL and `0.7x` weight, explicitly avoiding FTS pollution. FTS5 itself uses weighted BM25 over title, trigger phrases, file path, and content.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179746:- **What it does**: Engram pairs stable `topic_key` upserts with direct lookup in `Search()`, so an evolving architecture or bug thread can be retrieved deterministically by key instead of approximately by meaning. Public has artifact-aware routing and strong semantic search, but no equivalent first-class thread-key lookup inside `memory_search`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179753:- Fallback note: CocoIndex was unavailable in-session for this pass, so the analysis used targeted grep plus direct file reads.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179756:Design a concrete routing matrix for Public: `exact key / artifact name -> lexical-first`, `trigger phrase -> trigger lane`, `short exact query -> lexical-preserving hybrid`, `natural-language concept query -> semantic-first hybrid`, then decide whether thread-key lookup belongs inside `memory_search` or as a sibling surface.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179779:- **Why it matters**: Public already has the underlying recovery and context machinery (`session_bootstrap`, `session_resume`, `session_health`, `memory_context`), but its setup story is comparatively fragmented across MCP tools, plugins, code-graph, CocoIndex, and `generate-context.js`. The DX lesson is to add a single setup/export layer per runtime that installs the right bootstrap instructions and default recovery path on top of the existing system.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179807:- **Why it matters**: Debuggability is not only about runtime checks; it is also about reducing uncertainty during setup and recovery. Public should steal Engram’s habit of packaging the happy path and the fallback path together, ideally with a single setup/doctor document or command that points to `session_bootstrap`, `session_health`, `memory_health`, graph status, and CocoIndex status in one place.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179820:- Fallback note: CocoIndex/semantic search was permission-blocked for this external path in-session, so this pass used targeted grep plus direct file reads.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179874:- **What it does**: Public already measures memory totals/statuses/tier breakdowns, trigger counts, embedding retry state, FTS drift, repair actions, session quality, code-graph freshness, CocoIndex readiness, causal-link coverage, and deep-loop convergence signals.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179884:  3. **System health**: embedding readiness, vector availability, FTS parity, alias conflicts, session quality, graph freshness, code-graph parse health, CocoIndex availability, causal coverage, convergence blockers.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179891:- Fallback note: CocoIndex/semantic search was permission-blocked for this external path in-session, so this pass used targeted grep plus direct file reads.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:179996:- **Why it matters**: Public already has the better memory core; what it lacks is a similarly easy install/bootstrap/export story. This should be a delivery-layer improvement over existing `session_bootstrap`, `session_resume`, `memory_context`, and health surfaces.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180013:### Finding 4: Add a read-only doctor/scorecard surface over existing diagnostics instead of widening `memory_search`
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180080:✗ memory_match_triggers (MCP: spec_kit_memory) · prompt: "DEEP RESEARCH iteration 31 of 40 on exter…
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180268:● Deep-research(gpt-5.4) Drafting roadmap research
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180740:- **What it does**: Engram does direct-key lookup plus one sanitized FTS5 query ordered by `fts.rank`. Public runs vector/FTS/BM25/graph/degree sequentially, may rerank, waits for embeddings on cache miss, dedups across sessions, and routes low-latency cases into `memory_match_triggers` or smaller channel subsets.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180764:- **What it does**: Engram startup is mostly SQLite open, pragmas, migrations, then a bounded formatter over recent sessions/prompts/observations. Public startup/resume already composes `memory_context`, graph status, CocoIndex availability, health hints, pending-file recovery, and optional startup indexing.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180808:- **What did not work**: CocoIndex and memory-context retrieval were unavailable in this environment, so semantic lookup had to be replaced with direct file-path reads.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180827:COMPATIBILITY ANALYSIS: How do the adopted patterns interact with our existing CocoIndex, code-graph, and MCP tool stack? Conflict analysis.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180833:- **What it does**: Engram separates agent-facing and admin-facing tools, then reinforces that split with eager/deferred instructions. Public already exposes a larger orchestrated surface: `session_resume`, `session_bootstrap`, `code_graph_query`, `code_graph_context`, and CocoIndex maintenance/status tools alongside memory tools.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180841:- **What it does**: Engram exposes recent sessions, prompts, and observations through `mem_context`, plus explicit lifecycle tools like `mem_session_start`, `mem_session_end`, and `mem_session_summary`. Public already composes memory, code-graph state, CocoIndex availability, structural trust, and transport guidance into `session_resume` and `session_bootstrap`.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180849:- **What it does**: Engram checks exact `topic_key` matches first when the query looks key-like, then falls back to FTS. Public already routes queries across vector/FTS/BM25/graph/degree channels and separately nudges structural questions toward `code_graph_query` and semantic concept exploration toward CocoIndex-backed flows.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180850:- **Why it matters**: A future `thread_key` lookup can be a cheap compatibility win because it trims work for exact artifacts, stable threads, and session-summary lookups. The conflict appears only if that lexical fast path expands too far and starts capturing questions that should go to CocoIndex or code-graph instead.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180865:- **What it does**: Engram tells agents to recover from compaction by calling `mem_context` and then continuing under the memory protocol. Public's recovery path is intentionally broader: `session_bootstrap` and `session_resume` expose structural readiness, graph freshness, CocoIndex availability, and explicit routing to `code_graph_query` or semantic search.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180866:- **Why it matters**: Copying Engram's recovery text literally would flatten Public's richer retrieval stack back into memory-only recovery. That would make startup continuity simpler, but wrong: agents could recover memory and still miss stale graph state, absent CocoIndex, or the need to route structural questions away from Grep.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180898:- **Questions addressed**: tool-profile compatibility; session-lifecycle compatibility; exact-key/thread-key fit with hybrid routing; runtime setup fit with MCP stack; compaction conflict with code-graph and CocoIndex recovery
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180903:- Literal agent/admin tool reduction that hides `code_graph_query`, `code_graph_context`, or CocoIndex maintenance behind a memory-only profile, because that would erase core routing surfaces Public already depends on.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:180909:- **What did not work**: CocoIndex semantic code search was unavailable in this environment (`Permission denied and could not request permission from user`), so the comparison had to fall back to direct source reads and targeted grep instead of live semantic traversal.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181209:  │ "generate-context\.js|session_bootstrap|session_resume|memory_context\(|/memory:save|/spec_kit:r
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181210:  │ esume|memory_index_scan|code_graph_query|CocoIndex|code graph" in **/*.{md,ts,js,json,sh}
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181367:That bundle contains the missing Level 3 docs, the full **Iteration 036: USER WORKFLOW IMPACT** writeup, and the exact `research.md` insertion block. The main conclusions from iteration 036 are: **adopt now** one-command runtime setup + action-card, a thin close-session helper, an additive recent-session digest, and a migration crosswalk; **prototype later** a profile-aware starter workflow and an opt-in passive-capture helper. **CocoIndex was unavailable** in this runtime, so the pass used direct file reads plus `rg` fallback.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181647:**Content outcome:** the iteration delivers explicit **BEFORE/AFTER ASCII architecture maps** and grounds the production delta in four adopt-now changes: an additive recent-session digest inside `session_resume`/`session_bootstrap`, a thin close-session digest emission path, an exact `thread_key` fast lane ahead of the hybrid router, and one-command runtime setup plus action-card wrappers. It also states the invariants that do **not** change: hybrid retrieval stays primary, `code_graph_query`/`code_graph_context` and CocoIndex stay first-class, `generate-context.js` plus `memory_index_scan` remain the file-first save/index path, and no second lifecycle authority is introduced.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181683:- **What it does**: Engram proves that smaller agent/admin bundles reduce clutter and make onboarding easier. Public, however, derives much of its value from the coexistence of `session_bootstrap`, `session_resume`, `code_graph_query`, `code_graph_context`, and CocoIndex-aware routing. The unresolved question is how to package those capabilities for agents without collapsing back to a memory-only recovery and discovery model.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181699:- **What it does**: The run already established that Public should expose a read-only composite scorecard rather than widen `memory_search`. The remaining questions are operational: which existing surfaces are mandatory in v1, whether any repair hints can appear without repair side effects, and what shadow-mode thresholds are required before digest, exact-handle, and packaging changes graduate from experiment to default behavior.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181773:- **What it does**: Engram separates agent/admin tools and keeps explicit `mem_context` and session/save surfaces; Mnemosyne splits project/global/core recall-store-delete; MemPalace splits status/taxonomy/search/write tools; Spec Kit separates `memory_context`, `memory_search`, `memory_match_triggers`, `memory_health`, and session bootstrap/resume. Mex is the outlier: it pushes most control-plane behavior into `CLAUDE.md` -> `ROUTER.md` -> context/pattern scaffold files plus CLI verbs instead of a live memory MCP surface.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181782:- **Why it matters**: The transferable pattern is layered warm-up discipline at startup and compaction boundaries, not any single bootstrap format. Public should keep `memory_context` and `session_bootstrap` as the authorities and treat any recent-session digest or action-card addition as a bounded additive layer.
.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/001-engram-main/research/research.md:181873:- Replacing `session_bootstrap` / `memory_context` with a router-first markdown bootstrap, because Public already has a richer orchestration authority than Mex-style scaffold routing.

 succeeded in 2823ms:
2026-04-27 16:47:16.282 xcodebuild[60216:5634215]  DVTFilePathFSEvents: Failed to start fs event stream.
2026-04-27 16:47:16.486 xcodebuild[60216:5634205] [MT] DVTDeveloperPaths: Failed to get length of DARWIN_USER_CACHE_DIR from confstr(3), error = Error Domain=NSPOSIXErrorDomain Code=5 "Input/output error". Using NSCachesDirectory instead.
python3: warning: confstr() failed with code 5: couldn't get path of DARWIN_USER_TEMP_DIR; using /tmp instead
python3: error: couldn't create cache file '/tmp/xcrun_db-jH2r0ET5' (errno=Operation not permitted)
2026-04-27 16:47:16.916 xcodebuild[60314:5634443]  DVTFilePathFSEvents: Failed to start fs event stream.
2026-04-27 16:47:17.028 xcodebuild[60314:5634440] [MT] DVTDeveloperPaths: Failed to get length of DARWIN_USER_CACHE_DIR from confstr(3), error = Error Domain=NSPOSIXErrorDomain Code=5 "Input/output error". Using NSCachesDirectory instead.
[]

codex
The first grep was too broad and hit archived research, so I’m narrowing to live-ish implementation surfaces: Spec Kit Memory MCP, CocoIndex MCP, command docs, and the compact code graph specs.
exec
/bin/zsh -lc "rg -n \"memory_search|memory_context|CocoIndex|code_graph_context|hybrid|FTS|BM25|search\" .opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement .opencode/specs/system-spec-kit/024-compact-code-graph .opencode/specs/system-spec-kit/026* .opencode/specs/system-spec-kit/027* .opencode/specs/system-spec-kit/028* --glob 'spec.md' --glob 'plan.md' --glob 'implementation-summary.md' --glob 'decision-record.md' --glob 'description.json'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 exited 1 in 0ms:
zsh:1: no matches found: .opencode/specs/system-spec-kit/027*

exec
/bin/zsh -lc "rg -n \"memory_search|memory_context|memory_match_triggers|hybrid|FTS|BM25|CocoIndex|code_graph_context|code_graph_query|search\" .opencode/skills/system-spec-kit/mcp_server .opencode/skills/mcp-coco-index .opencode/commands/memory .opencode/agents/context.md --glob '"'!**/node_modules/**'"' --glob '"'!**/dist/**'"'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
.opencode/agents/context.md:27:Read-only context retrieval agent. The **exclusive entry point for ALL exploration tasks** — every codebase search, file discovery, pattern analysis, and context retrieval routes through this agent. Gathers structured Context Packages before implementation begins. Executes retrieval directly and NEVER performs nested delegation. NEVER writes, edits, creates, or deletes files.
.opencode/agents/context.md:49:3. **GRAPH HEALTH** → Call `code_graph_status()` once per session before structural exploration so the agent knows whether code graph tools are usable or whether CocoIndex/filesystem fallbacks are required
.opencode/agents/context.md:50:4. **CODEBASE SCAN** → Prefer `code_graph_query` / `code_graph_context` for structural questions, then CocoIndex, Glob, Grep, and Read as needed
.opencode/agents/context.md:66:| `Grep`                  | Codebase    | Text/code pattern search  | Find keywords, function calls, usage |
.opencode/agents/context.md:67:| `CocoIndex search`      | Semantic    | Concept-based code discovery | Find code by intent, not exact text |
.opencode/agents/context.md:70:| `memory_match_triggers` | Memory (L2) | Trigger phrase matching   | Quick context surfacing (Layer 1)    |
.opencode/agents/context.md:71:| `memory_context`        | Memory (L1) | Unified context retrieval | Intent-aware routing (Layer 1/3)     |
.opencode/agents/context.md:72:| `memory_search`         | Memory (L2) | 3-channel hybrid search (Vector, BM25, FTS5) with RRF fusion | Deep memory retrieval (Layer 3) |
.opencode/agents/context.md:74:| `code_graph_query`      | Structure   | Graph traversal           | Structural questions: calls, imports, impact |
.opencode/agents/context.md:75:| `code_graph_context`    | Structure   | Compact graph context     | Neighborhood/outline context around structural seeds |
.opencode/agents/context.md:88:    │   └─► Grep → search for text patterns
.opencode/agents/context.md:91:    │   └─► CocoIndex search → find code by meaning
.opencode/agents/context.md:97:    │   └─► memory_match_triggers → memory_search
.opencode/agents/context.md:100:    │   └─► memory_context → unified retrieval
.opencode/agents/context.md:123:**Tool Sequence**: `memory_match_triggers` → `memory_context(deep)` → `code_graph_status()` → `memory_search(includeContent)` → `code_graph_query/context` for structural questions → `CocoIndex search` (1-3 concept queries) → `Glob` (5-10 patterns) → `Grep` (3-5 patterns) → `Read` (5-8 key files) → spec folder analysis → `memory_list(specFolder)`
.opencode/agents/context.md:137:**Sources**: `handover.md`, `_memory.continuity`, packet spec docs, then `memory_match_triggers`, `memory_context`
.opencode/agents/context.md:145:- Run `memory_match_triggers(prompt)` to surface saved rules and prior work that may affect the current task
.opencode/agents/context.md:146:- Run `memory_context({ input: topic, mode: "deep" })` only when packet-local continuity still leaves gaps or broader history is needed
.opencode/agents/context.md:152:**Tools**: `code_graph_status`, `code_graph_query`, `code_graph_context`, `Glob`, `Grep`, `Read`
.opencode/agents/context.md:155:- **Code graph** — Run `code_graph_status()` once per session, then use `code_graph_query` / `code_graph_context` for structural questions when the index is healthy.
.opencode/agents/context.md:156:- **CocoIndex** — Semantic search for concept-based discovery. Use 1-3 short queries (3-5 words). Examples: `ccc search "authentication middleware"`, `ccc search "error handling patterns"`. Set `refresh_index=false` after first query. (Verify the binary is the spec-kit fork: `ccc --version` should report `0.2.3+spec-kit-fork.0.2.0` — the fork emits dedup + path-class fields used by ranking interpretation; if the substring `+spec-kit-fork.` is missing, run `bash .opencode/skills/mcp-coco-index/scripts/install.sh` to recover.)
.opencode/agents/context.md:158:- **Grep** — Find specific usage within discovered paths. Use file paths from Glob to narrow search scope. Examples: `authenticate(`, `import.*auth`
.opencode/agents/context.md:165:**Tools**: `memory_search`, `memory_context (deep)`, `memory_list`
.opencode/agents/context.md:167:**Strategy**: Comprehensive semantic search to complement Layers 1-2:
.opencode/agents/context.md:168:- `memory_search({ query: topic, includeContent: true })` — 3-channel hybrid search (Vector, BM25, FTS5) with RRF fusion across all indexed spec-doc records with full content
.opencode/agents/context.md:169:- `memory_context({ input: topic, mode: "deep" })` — comprehensive retrieval with full analysis, ranked intent-aware results
.opencode/agents/context.md:237:[proceed | research-deeper | ask-user]
.opencode/agents/context.md:238:- **Verdict**: [proceed / research-deeper / ask-user]
.opencode/agents/context.md:313:| NEVER claim "nothing found" without actual searches across memory/codebase | HARD BLOCK  |
.opencode/agents/context.md:336:- Claim "nothing found" without actually searching
.opencode/agents/context.md:366:When the query intent is semantic (find code by concept, understand implementations, discover patterns), ALWAYS try CocoIndex FIRST before falling back to Grep/Glob:
.opencode/agents/context.md:368:1. **Semantic discovery** ("find code that...", "how is X implemented", "similar to") → `mcp__cocoindex_code__search` FIRST
.opencode/agents/context.md:369:2. Only if CocoIndex unavailable or returns no results → fall back to Grep/Glob
.opencode/agents/context.md:370:3. **Structural queries** ("what calls...", "what imports...") → `code_graph_query` / `code_graph_context`
.opencode/agents/context.md:388:| @deep-research | `.opencode/agents/deep-research.md` | Deeper alternative — when @context finds complexity requiring iterative multi-round investigation |
.opencode/agents/context.md:396:| `memory_context`        | L1    | Unified entry point for context retrieval |
.opencode/agents/context.md:397:| `memory_match_triggers` | L2    | Fast trigger phrase matching              |
.opencode/agents/context.md:398:| `memory_search`         | L2    | 3-channel hybrid search (Vector, BM25, FTS5) with RRF fusion |
.opencode/agents/context.md:407:| `mcp-coco-index`  | Semantic code search via vector embeddings          |
.opencode/agents/context.md:413:If hook-injected context is present (from Claude Code SessionStart hook), use it directly. Do NOT redundantly call `memory_context` or `memory_match_triggers` for the same information. If hook context is NOT present, recover prior work in `/spec_kit:resume` order: read `handover.md`, then `_memory.continuity`, then the relevant spec docs. Use `memory_context({ mode: "resume", profile: "resume" })` and `memory_match_triggers()` only when packet-local continuity is missing, ambiguous, or needs broader repo history.
.opencode/agents/context.md:415:Route queries by intent: CocoIndex (`mcp__cocoindex_code__search`) for semantic discovery, Code Graph (`code_graph_query`/`code_graph_context`) for structural navigation, Memory (`memory_search`/`memory_context`) for session continuity.
.opencode/agents/context.md:429:│  └─► Exploration routing guardrail for all codebase searches            │
.opencode/agents/context.md:432:│  ├─► Layer 1: memory_match_triggers and memory_context                  │
.opencode/agents/context.md:434:│  └─► Layer 3: deep memory search with spec cross-reference              │
.opencode/commands/memory/README.txt:3:description: "Slash commands for managing the Spec Kit Memory system including search, session recovery, constitutional memory management, database operations, and async ingestion."
.opencode/commands/memory/README.txt:7:  - "memory search"
.opencode/commands/memory/README.txt:63:| **search** | `/memory:search <query> [--intent:<type>]` or `/memory:search <subcommand>` | Unified retrieval and analysis: intent-aware search, epistemic baselines, causal graph, ablation, dashboard |
.opencode/commands/memory/README.txt:94:| preflight | `/memory:search preflight <specFolder> <taskId>` | Capture epistemic baseline before task |
.opencode/commands/memory/README.txt:95:| postflight | `/memory:search postflight <specFolder> <taskId>` | Calculate learning delta after task |
.opencode/commands/memory/README.txt:96:| causal | `/memory:search causal <memoryId>` | Trace causal chain for a memory |
.opencode/commands/memory/README.txt:97:| link | `/memory:search link <source> <target> <relation>` | Create causal relationship |
.opencode/commands/memory/README.txt:98:| unlink | `/memory:search unlink <edgeId>` | Remove causal relationship |
.opencode/commands/memory/README.txt:99:| causal-stats | `/memory:search causal-stats` | View causal graph statistics |
.opencode/commands/memory/README.txt:100:| ablation | `/memory:search ablation` | Run channel ablation study |
.opencode/commands/memory/README.txt:101:| dashboard | `/memory:search dashboard` | View reporting dashboard |
.opencode/commands/memory/README.txt:102:| history | `/memory:search history <specFolder>` | View learning history and LI trends |
.opencode/commands/memory/README.txt:114:├── search.md       # /memory:search - Unified retrieval + analysis (intent-aware search, epistemic, causal, eval)
.opencode/commands/memory/README.txt:134:/memory:search "how does the auth system work"
.opencode/commands/memory/README.txt:137:/memory:search "auth flow" --intent:fix_bug
.opencode/commands/memory/README.txt:167:/memory:search history specs/007-auth
.opencode/commands/memory/README.txt:170:/memory:search preflight specs/007-auth T1
.opencode/commands/memory/README.txt:173:/memory:search postflight specs/007-auth T1
.opencode/commands/memory/README.txt:176:/memory:search causal 42
.opencode/commands/memory/README.txt:179:/memory:search link 42 43 caused
.opencode/commands/memory/README.txt:182:/memory:search causal-stats
.opencode/commands/memory/README.txt:185:/memory:search ablation
.opencode/commands/memory/README.txt:188:/memory:search dashboard
.opencode/commands/memory/README.txt:231:> **026 Note:** Tool count increased from 33 to 47 with the addition of session management tools (`session_bootstrap`, `session_health`, `session_resume`), code graph tools (`code_graph_query`, `code_graph_scan`, `code_graph_status`, `code_graph_context`), and CCC tools (`ccc_status`, `ccc_feedback`, `ccc_reindex`). Graph-first retrieval routing (026) means `code_graph_query` is now the preferred first channel for structural code search before semantic/vector or FTS5/BM25 fallback.
.opencode/commands/memory/README.txt:235:| 1 | `memory_context` | L1 | `/memory:search` |
.opencode/commands/memory/README.txt:236:| 2 | `memory_quick_search` | L2 | `/memory:search` |
.opencode/commands/memory/README.txt:237:| 3 | `memory_search` | L2 | `/memory:search` |
.opencode/commands/memory/README.txt:238:| 4 | `memory_match_triggers` | L2 | `/memory:search` |
.opencode/commands/memory/README.txt:251:| 17 | `task_preflight` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:252:| 18 | `task_postflight` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:253:| 19 | `memory_drift_why` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:254:| 20 | `memory_causal_link` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:255:| 21 | `memory_causal_stats` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:256:| 22 | `memory_causal_unlink` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:257:| 23 | `eval_run_ablation` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:258:| 24 | `eval_reporting_dashboard` | L6 | `/memory:search` |
.opencode/commands/memory/README.txt:260:| 26 | `memory_get_learning_history` | L7 | `/memory:search` |
.opencode/commands/memory/README.txt:267:| 33 | `code_graph_query` | L2 | `/memory:search` |
.opencode/commands/memory/README.txt:270:| 36 | `code_graph_context` | L2 | `/memory:search` |
.opencode/commands/memory/README.txt:278:| `/memory:search` | 15 | (none) | L1, L2, L6, L7 |
.opencode/commands/memory/README.txt:280:| `/memory:manage` | 20 | 1 (search) | L3, L4, L5, L7 |
.opencode/commands/memory/README.txt:282:| `/spec_kit:resume` | 3 | uses search/manage tools | L1 |
.opencode/commands/memory/README.txt:294:**Q: What is the difference between `/memory:search` and `/spec_kit:resume`?**
.opencode/commands/memory/README.txt:296:`/memory:search` retrieves and searches indexed knowledge using a query or subcommand. `/spec_kit:resume` handles session continuation and interrupted-session recovery: it reconstructs packet context from `handover.md`, then `_memory.continuity`, then canonical spec docs before deeper memory tools engage. Use `search` for knowledge lookup and `resume` when you need to continue prior work.
.opencode/commands/memory/README.txt:300:Use `/memory:learn` to create constitutional memories: short, always-surface rules that appear at the top of every search result (e.g., coding standards, project constraints). Use `/memory:save` to preserve session context, implementation decisions, and research findings tied to a specific spec folder. Constitutional memories apply globally. Saved context is scoped to a spec folder.
.opencode/commands/memory/README.txt:317:| Resume finds no session | No saved context from prior session | Use `/spec_kit:plan` to start fresh or `/memory:search` with a manual query |
.opencode/commands/memory/README.txt:324:| History returns empty | No PREFLIGHT/POSTFLIGHT records | Use `/memory:search preflight` before tasks, view with `/memory:search history` |
.opencode/commands/memory/save.md:65:Save the current conversation context, including session summary, key decisions, modified files, and trigger phrases, into the packet's canonical continuity surfaces so `/spec_kit:resume` and `/memory:search` read the same source of truth.
.opencode/commands/memory/save.md:96:| `research_finding` | `research/research.md::findings` | Evidence, investigation result, cited upstream behavior |
.opencode/commands/memory/save.md:230:- **Trigger phrases**: 5-10 keywords/phrases for future semantic search retrieval
.opencode/commands/memory/save.md:269:| `research`       | Investigation findings   | `research-lenis-scroll-006`         |
.opencode/commands/memory/save.md:336:| `triggerPhrases`   | 5-12 items | Keywords for semantic search. Parser-enforced cap at 12. |
.opencode/commands/memory/save.md:353:> **Auto-index of touched files (Step 11.5):** After the canonical save updates packet docs and `graph-metadata.json`, the workflow runs an incremental `memory_index_scan` scoped to the target spec folder. This re-indexes any canonical spec docs (`spec.md`, `plan.md`, `tasks.md`, `checklist.md`, `decision-record.md`, `implementation-summary.md`, `handover.md`, `research/research.md`, `resource-map.md`) and `graph-metadata.json` that were modified earlier in the session. Incremental mode skips unchanged files cheaply via mtime + content-hash checks.
.opencode/commands/memory/save.md:423:    "anchors_updated": ["summary-011", "decision-vector-search-011", "files-011"],
.opencode/commands/memory/save.md:424:    "trigger_phrases": ["semantic search", "vector embeddings", "memory retrieval"],
.opencode/commands/memory/save.md:428:    "Use /memory:search to find the updated packet context later",
.opencode/commands/memory/save.md:523:| Search indexed continuity    | `/memory:search [query]`                | Find related context          |
.opencode/commands/memory/save.md:532:- `/memory:search`: Intent-aware context retrieval and analysis tools
.opencode/commands/memory/save.md:609:| MCP server unreachable | Restart OpenCode to restart MCP server. Post-026: run `memory_health()` after restart to verify all retrieval channels (graph, vector, FTS5) are operational |
.opencode/skills/mcp-coco-index/mcp_server/MAINTENANCE.md:3:> Steps for merging a new upstream `cocoindex-code` release into the spec-kit fork while preserving the patches from `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/011-mcp-runtime-stress-remediation/004-cocoindex-overfetch-dedup-rerank/` (the cocoindex-overfetch-dedup packet — currently numbered `004`; tracked as `009` during research and in commit history).
.opencode/skills/mcp-coco-index/mcp_server/MAINTENANCE.md:9:This guide explains how to pull a new upstream `cocoindex-code` release into the vendored soft-fork at `.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/` without losing the spec-kit fork patches (REQ-001..006). Those patches were authored in `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/011-mcp-runtime-stress-remediation/004-cocoindex-overfetch-dedup-rerank/` — the cocoindex-overfetch-dedup packet, currently numbered `004` in the renumbered phase tree (tracked as `009` during research and in commit history such as `1b62e976d`). The workflow uses `scripts/update.sh` to surface diffs, then walks through manual merge, version bump, attribution updates, reinstall, and acceptance probes.
.opencode/skills/mcp-coco-index/mcp_server/MAINTENANCE.md:90:ccc search "semantic search vector embedding implementation" --limit 10
.opencode/skills/mcp-coco-index/mcp_server/MAINTENANCE.md:93:ccc search "code graph traversal callers query" --limit 10
.opencode/commands/memory/manage.md:4:allowed-tools: Read, spec_kit_memory_memory_stats, spec_kit_memory_memory_list, spec_kit_memory_memory_search, spec_kit_memory_memory_index_scan, spec_kit_memory_memory_validate, spec_kit_memory_memory_update, spec_kit_memory_memory_delete, spec_kit_memory_memory_bulk_delete, spec_kit_memory_memory_health, spec_kit_memory_checkpoint_create, spec_kit_memory_checkpoint_restore, spec_kit_memory_checkpoint_list, spec_kit_memory_checkpoint_delete, spec_kit_memory_memory_ingest_start, spec_kit_memory_memory_ingest_status, spec_kit_memory_memory_ingest_cancel
.opencode/commands/memory/manage.md:64:**Separation from `/memory:search`:**
.opencode/commands/memory/manage.md:65:- `/memory:search` = RETRIEVAL + ANALYSIS (intent-aware search, epistemic baselines, causal graph, evaluation)
.opencode/commands/memory/manage.md:201:> **Retrieval Metrics (P2):** Additional internal retrieval metrics are tracked by the search pipeline; dashboard exposure remains deferred until handler wiring is completed.
.opencode/commands/memory/manage.md:380:| `--apply` | Applies the cleanup transactionally: deletes rows on excluded paths and downgrades non-constitutional `constitutional` rows to `important`. Each change writes a durable `governance_audit` row (`tier_downgrade_non_constitutional_path_cleanup` action). FTS cleanup is delegated to the `memory_index` trigger; the CLI does not touch `memory_fts` directly. The authoritative plan is rebuilt inside `database.transaction(...)` — pre-transaction plans are not trusted. |
.opencode/commands/memory/manage.md:892:- `/memory:search`: Intent-aware context retrieval and analysis tools
.opencode/commands/memory/manage.md:928:spec_kit_memory_memory_search({ query: "<q>", limit: N, specFolder: "optional" })
.opencode/commands/memory/manage.md:944:> **Feature Flag Behavior:** `SPECKIT_ADAPTIVE_FUSION` affects scan and search behavior: when enabled, index scans apply adaptive weight profiles during embedding and artifact-class routing during re-indexing. `SPECKIT_EXTENDED_TELEMETRY` enables detailed per-operation metrics for scan, search, and health calls. **Mutation Ledger:** cleanup and delete operations are recorded in the append-only mutation ledger, providing a full audit trail that can be reviewed when investigating unexpected state changes.
.opencode/commands/memory/manage.md:977:| `autoRepair` | boolean | false | Attempt best-effort repair actions (e.g., FTS rebuild) |
.opencode/commands/memory/manage.md:1000:| `resultRank` | number | No | Rank position (1-based) of the selected memory in search results |
.opencode/commands/memory/manage.md:1002:| `searchMode` | string | No | Search mode context (`search`, `context`, `trigger`) |
.opencode/commands/memory/learn.md:2:description: Create and manage constitutional rules — always-surface entries that appear at the top of every search result.
.opencode/commands/memory/learn.md:4:allowed-tools: Read, Write, Edit, Glob, Bash, spec_kit_memory_memory_save, spec_kit_memory_memory_search, spec_kit_memory_memory_stats, spec_kit_memory_memory_list, spec_kit_memory_memory_delete, spec_kit_memory_memory_index_scan
.opencode/commands/memory/learn.md:45:Create, list, edit, and remove **constitutional rules**, the highest-tier entries that surface at the top of every search result, never decay, and carry a 3.0x search boost.
.opencode/commands/memory/learn.md:51:Provide a dedicated command for managing constitutional rules, the most powerful tier in the Spec Kit Memory system. Constitutional rules always appear at the top of every `memory_search()` result and never decay. This command handles the full lifecycle: creation with proper frontmatter and ANCHOR format, budget validation, editing, and removal.
.opencode/commands/memory/learn.md:61:| Surfaces in | EVERY search | Relevant only | Relevant only |
.opencode/commands/memory/learn.md:142:  Constitutional rules appear in EVERY search
.opencode/commands/memory/learn.md:181:*Constitutional Memory — Always surfaces at top of search results*
.opencode/commands/memory/learn.md:224:   memory_search({ query: "<one trigger phrase>", limit: 3 })
.opencode/commands/memory/learn.md:410:  This rule will NO LONGER surface in search results.
.opencode/commands/memory/learn.md:501:- `/memory:search`: Intent-aware context retrieval and analysis tools
.opencode/commands/memory/learn.md:519:| Index new file | `memory_save({ filePath, force: true })` | Add to search index |
.opencode/commands/memory/learn.md:520:| Verify surfaces | `memory_search({ query })` | Confirm isConstitutional: true |
.opencode/commands/memory/search.md:2:description: Unified continuity retrieval and analysis - canonical spec-doc context search, epistemic baselines, causal graph, ablation studies, and dashboards
.opencode/commands/memory/search.md:4:allowed-tools: Read, spec_kit_memory_memory_context, spec_kit_memory_memory_quick_search, spec_kit_memory_memory_search, spec_kit_memory_memory_match_triggers, spec_kit_memory_task_preflight, spec_kit_memory_task_postflight, spec_kit_memory_memory_drift_why, spec_kit_memory_memory_causal_link, spec_kit_memory_memory_causal_stats, spec_kit_memory_memory_causal_unlink, spec_kit_memory_eval_run_ablation, spec_kit_memory_eval_reporting_dashboard, spec_kit_memory_memory_get_learning_history
.opencode/commands/memory/search.md:55:Unified entry point for knowledge retrieval and analysis. Combines intent-aware context search (retrieval mode) with epistemic measurement, causal graph tools, and evaluation dashboards (analysis mode).
.opencode/commands/memory/search.md:87:- Applies task-specific weights for search optimization
.opencode/commands/memory/search.md:88:- Combines search + load in a single operation
.opencode/commands/memory/search.md:102:The unified context tool runs a hybrid retrieval pipeline with **graph-first routing** (026):
.opencode/commands/memory/search.md:104:- **Graph channel has priority** in the fusion strategy: structural queries (callers, imports, dependencies) are routed to `code_graph_query` first, before semantic or lexical channels
.opencode/commands/memory/search.md:105:- Tri-channel retrieval (graph + vector/semantic + FTS5/BM25) with graph results given precedence in the fusion merge
.opencode/commands/memory/search.md:106:- CocoIndex semantic search (`mcp__cocoindex_code__search`) integrates as the vector/semantic channel, providing natural-language code discovery alongside indexed-continuity vector search
.opencode/commands/memory/search.md:107:- When graph and semantic channels miss or return weak results, a 3-tier FTS fallback activates: FTS5 full-text → BM25 keyword scoring → Grep/Glob filesystem search. Post-026 FTS5 remediation improved BM25 tokenization and ranking accuracy
.opencode/commands/memory/search.md:137:| `/memory:search "implement auth"` | Auto-detect add_feature, apply weights |
.opencode/commands/memory/search.md:138:| `/memory:search "auth bug" --intent:fix_bug` | Explicit fix_bug intent |
.opencode/commands/memory/search.md:139:| `/memory:search "how does auth work?"` | Auto-detect understand intent |
.opencode/commands/memory/search.md:140:| `/memory:search "optimize auth code"` | Auto-detect refactor intent |
.opencode/commands/memory/search.md:141:| `/memory:search "auth security review"` | Auto-detect security_audit intent |
.opencode/commands/memory/search.md:142:| `/memory:search "find the spec for auth"` | Auto-detect find_spec intent |
.opencode/commands/memory/search.md:143:| `/memory:search "why did we choose JWT"` | Auto-detect find_decision intent |
.opencode/commands/memory/search.md:149:| `/memory:search preflight specs/007-auth T1` | Capture epistemic baseline |
.opencode/commands/memory/search.md:150:| `/memory:search postflight specs/007-auth T1` | Calculate learning delta |
.opencode/commands/memory/search.md:151:| `/memory:search history specs/007-auth` | View learning history |
.opencode/commands/memory/search.md:152:| `/memory:search causal 42` | Trace causal chain for memory #42 |
.opencode/commands/memory/search.md:153:| `/memory:search link 42 43 caused` | Link memory #42 → #43 as caused |
.opencode/commands/memory/search.md:154:| `/memory:search unlink 5` | Remove causal edge #5 |
.opencode/commands/memory/search.md:155:| `/memory:search causal-stats` | View causal graph statistics |
.opencode/commands/memory/search.md:156:| `/memory:search ablation` | Run channel ablation study |
.opencode/commands/memory/search.md:157:| `/memory:search dashboard` | View reporting dashboard |
.opencode/commands/memory/search.md:282:Adjust search parameters:
.opencode/commands/memory/search.md:290:spec_kit_memory_memory_context({
.opencode/commands/memory/search.md:326:- **Leaf folder name only** as group header (last path segment, e.g., `010-search-retrieval-quality-fixes/`)
.opencode/commands/memory/search.md:329:- If two leaf names collide, prefix with parent number: `023/010-search-quality/`
.opencode/commands/memory/search.md:336:When semantic + lexical search return zero direct matches but the trigger-phrase matcher OR constitutional-rule surfacer returned spec-doc records, render them under explicit canonical labels — never invent ad-hoc wording like "Auto-triggered memories":
.opencode/commands/memory/search.md:342:No spec-doc records matched this query via semantic or lexical search.
.opencode/commands/memory/search.md:365:The following phrases MUST NOT appear anywhere in any `/memory:search` rendering — empty-result fallback, full-result render, or analysis subcommand output. This list is authoritative; treat any occurrence as a P0 contract violation.
.opencode/commands/memory/search.md:391:**memory_context L1 Budget:** ~2000 tokens total (mode-managed)
.opencode/commands/memory/search.md:466:**Trigger:** `/memory:search preflight <specFolder> <taskId>`
.opencode/commands/memory/search.md:512:**Trigger:** `/memory:search postflight <specFolder> <taskId>`
.opencode/commands/memory/search.md:566:**Trigger:** `/memory:search history <specFolder>`
.opencode/commands/memory/search.md:606:**Trigger:** `/memory:search causal <memoryId>`
.opencode/commands/memory/search.md:641:**Trigger:** `/memory:search link <sourceId> <targetId> <relation>`
.opencode/commands/memory/search.md:671:**Trigger:** `/memory:search unlink <edgeId>`
.opencode/commands/memory/search.md:673:Removes a causal relationship by edge ID. Use `/memory:search causal <memoryId>` first to find edge IDs.
.opencode/commands/memory/search.md:694:**Trigger:** `/memory:search causal-stats`
.opencode/commands/memory/search.md:726:**Trigger:** `/memory:search ablation`
.opencode/commands/memory/search.md:767:**Trigger:** `/memory:search dashboard`
.opencode/commands/memory/search.md:808:| Search fails | Fall back to unweighted search |
.opencode/commands/memory/search.md:841:| Context (preferred) | `spec_kit_memory_memory_context({ input, ... })` | SINGLE | Fall back to manual search |
.opencode/commands/memory/search.md:842:| Quick search (optional) | `spec_kit_memory_memory_quick_search({ query, ... })` | SINGLE | Fall back to preferred/manual retrieval |
.opencode/commands/memory/search.md:843:| Trigger check | `spec_kit_memory_memory_match_triggers({ prompt: query })` | OPTIONAL | Continue without |
.opencode/commands/memory/search.md:844:| Search (manual) | `spec_kit_memory_memory_search({ query, anchors, includeContent: true })` | SINGLE | Show error msg |
.opencode/commands/memory/search.md:858:> **Note:** The dedicated `spec_kit_memory_memory_context()` tool provides unified intent-aware retrieval server-side. It accepts `input`, `mode`, `intent`, `specFolder`, governed retrieval params (`tenantId`, `userId`, `agentId`), `limit`, `sessionId`, `enableDedup`, `includeContent`, `includeTrace`, `tokenUsage`, and `anchors`. `spec_kit_memory_memory_quick_search()` also supports governed retrieval via `tenantId`, `userId`, and `agentId`. This is the recommended unified approach. The manual orchestration below is for advanced use cases requiring fine-grained control.
.opencode/commands/memory/search.md:860:> **Adaptive Fusion, Hybrid Routing & Telemetry:** Retrieval combines vector, FTS5/BM25, and graph channels, then applies intent-adaptive fusion and reranking. Results may be routed through artifact-class classification before scoring. When `SPECKIT_ADAPTIVE_FUSION` is enabled, weights adapt dynamically by intent, including the internal continuity profile (`0.52 / 0.18 / 0.07 / 0.23`) used for resume-style retrieval. When `SPECKIT_EXTENDED_TELEMETRY` is enabled, extended telemetry is captured (query timing, score distributions, fusion decisions) and written to the telemetry log, while `getRerankerStatus()` reports reranker latency and cache `hits` / `misses` / `staleHits` / `evictions`.
.opencode/commands/memory/search.md:868:spec_kit_memory_memory_context({
.opencode/commands/memory/search.md:879:// Option 2: Simplified search for fast query-only retrieval
.opencode/commands/memory/search.md:880:spec_kit_memory_memory_quick_search({
.opencode/commands/memory/search.md:889:// Option 3: Manual search with anchors (advanced - fine-grained control)
.opencode/commands/memory/search.md:890:spec_kit_memory_memory_search({
.opencode/commands/memory/search.md:921:| 1 | `memory_context` | L1 | Retrieval | (default) |
.opencode/commands/memory/search.md:922:| 2 | `memory_quick_search` | L2 | Retrieval | (default) |
.opencode/commands/memory/search.md:923:| 3 | `memory_search` | L2 | Retrieval | (default) |
.opencode/commands/memory/search.md:924:| 4 | `memory_match_triggers` | L2 | Retrieval | (default) |
.opencode/commands/memory/search.md:939:### memory_context: Full Parameters
.opencode/commands/memory/search.md:951:| `includeTrace` | boolean | false | Include provenance-rich trace data (scores, source, trace) in results when underlying `memory_search` is called |
.opencode/commands/memory/search.md:955:### memory_search: Advanced Parameters
.opencode/commands/memory/search.md:957:The full `memory_search` parameter surface is available when using Option 3 (manual search). Key advanced parameters:
.opencode/commands/memory/search.md:961:| `query` | string | - | Natural language search query (required unless `concepts` provided) |
.opencode/commands/memory/search.md:962:| `concepts` | string[] | - | 2-5 concept strings for multi-concept AND search (required unless `query` provided) |
.opencode/commands/memory/search.md:963:| `specFolder` | string | - | Limit search to specific spec folder |
.opencode/commands/memory/search.md:973:| `bypassCache` | boolean | false | Skip tool cache and force fresh search |
.opencode/commands/memory/search.md:985:### memory_match_triggers: Cognitive Parameters
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/schema.py:1:"""Data models for CocoIndex Code."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:28:    "Code search and codebase understanding tools."
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:33:    "Provides semantic search that understands meaning --"
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:60:    """Result from search tool."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:79:        name="search",
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:81:            "Semantic code search across the entire codebase"
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:95:    async def search(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:98:                "Natural language query or code snippet to search for."
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:119:                "Whether to incrementally update the index before searching."
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:143:                lambda: client.search(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:155:        """Check if search should wait before querying.
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:260:    async def search(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:282:        search_results = [
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:297:            search_results,
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:454:async def _search_with_wait(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:457:    """Stream search response, waiting for ongoing indexing first."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:461:        results = await registry.search(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:503:                return _search_with_wait(registry, req)
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py:505:            results = await registry.search(
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:77:import * as vectorIndex from './lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:82:import * as hybridSearch from './lib/search/hybrid-search.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:83:import { createUnifiedGraphSearchFn } from './lib/search/graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:84:import { isGraphUnifiedEnabled } from './lib/search/graph-flags.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:94:import * as sessionBoost from './lib/search/session-boost.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:95:import * as causalBoost from './lib/search/causal-boost.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:96:import * as bm25Index from './lib/search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:98:import { getSpecsBasePaths } from './lib/search/folder-discovery.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:104:} from './lib/search/graph-lifecycle.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:109:} from './lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:111:import { disposeLocalReranker } from './lib/search/local-reranker.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:133:import { isLearnedFeedbackEnabled } from './lib/search/learned-feedback.js';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:229:  'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:230:  'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:270:  preferredTool: 'code_graph_query';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:271:  secondaryTool: 'code_graph_context';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:336:    preferredTool: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:337:    secondaryTool: 'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:338:    message: 'Advisory only: this looks like a structural question. Prefer `code_graph_query` before Grep or Glob for callers, imports, outline, and dependency lookups.',
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:393:// Stores the last resolved session ID so non-search tools (e.g. memory_stats)
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:394:// that lack an explicit sessionId param can still correlate with a prior search.
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:736:    hints.push(`Code graph: ${pkg.codeGraphStatus}, CocoIndex: ${pkg.cocoIndexAvailable ? 'available' : 'not installed'}`);
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:801:    'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:802:    'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:818:        snap.sessionQuality === 'critical' ? 'call memory_context(resume)' : 'ready';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:830:  // resume, health, and code_graph_query (ready | stale | absent |
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:831:  // unavailable). code_graph_query is only recommended when structural
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:837:  lines.push('- If structural context shows "ready": code_graph_query is available for structural lookups');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:838:  lines.push('- If "stale": code_graph_query still works, but a session_bootstrap refresh is recommended');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:840:  lines.push('- If "unavailable" (DB unreachable / readiness probe failed): call memory_health for repair guidance instead of code_graph_query');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:844:  // code_graph_query is only surfaced when graph freshness is 'fresh' or
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:852:      routingRules.push('Semantic/concept code search → mcp__cocoindex_code__search');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:855:      routingRules.push('Structural queries (callers, imports, deps) → code_graph_query');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:943:    if (name === 'memory_context' && args.mode === 'resume') {
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:947:      recordMetricEvent({ kind: 'code_graph_query' });
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:973:      name === 'memory_context' && args.mode === 'resume';
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1026:    // REQ-014: Log follow_on_tool_use when a non-search tool is called after a recent search
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1028:    if (name !== 'memory_search' && name !== 'memory_context' && name !== 'memory_quick_search' && name !== 'session_health') {
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1040:    // Phase 024: Code-search redirect hint for memory tools
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1041:    if ((name === 'memory_search' || name === 'memory_context') && result && !result.isError && result.content?.[0]?.text) {
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1049:            existingHints.push('Tip: For code search queries, consider using mcp__cocoindex_code__search for semantic code search or code_graph_query for structural lookups.');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1813:    hybridSearch,
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1906:      console.error('[context-server] WARNING: Database has 0 memories — search will return no results until memories are saved');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1915:    hybridSearch.init(database, vectorIndex.vectorSearch, graphSearchFn);
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1917:    // Keep db-state reinitialization wiring aligned with startup search wiring.
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1940:    console.error('[context-server] Checkpoints, access tracker, hybrid search, session boost, and causal boost initialized');
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1942:    // P3-04: Rebuild BM25 index from database on startup
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1947:        console.error(`[context-server] BM25 index rebuilt from database: ${count} documents`);
.opencode/skills/system-spec-kit/mcp_server/context-server.ts:1950:        console.warn('[context-server] BM25 index rebuild failed:', message);
.opencode/skills/mcp-coco-index/mcp_server/README.md:1:# CocoIndex MCP Server (Soft-Fork)
.opencode/skills/mcp-coco-index/mcp_server/README.md:3:> Vendored Python source for the CocoIndex Code daemon and CLI, soft-forked from upstream and patched per the spec packet at `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/011-mcp-runtime-stress-remediation/004-cocoindex-overfetch-dedup-rerank/` (cocoindex-overfetch-dedup, currently numbered `004`; tracked as `009` during research and in commit history).
.opencode/skills/mcp-coco-index/mcp_server/README.md:9:This folder bundles a soft-fork of [`cocoindex-code`](https://github.com/cocoindex-io/cocoindex-code) v0.2.3 with patches from the spec packet at `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/011-mcp-runtime-stress-remediation/004-cocoindex-overfetch-dedup-rerank/` (cocoindex-overfetch-dedup, currently numbered `004`; tracked as `009` during research). The vendored source ships in `cocoindex_code/` and installs as an editable Python package via `pyproject.toml`. The Rust-based upstream `cocoindex` runtime stays on PyPI as a regular dependency.
.opencode/skills/mcp-coco-index/mcp_server/README.md:31:- REQ-004: `path_class` taxonomy (`implementation`, `tests`, `docs`, `spec_research`, `generated`, `vendor`).
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/project.py:1:"""Project management: wraps a CocoIndex Environment + App."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/project.py:114:                name="CocoIndexCode",
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:17:**Graph as a first-class feature family.** The `SPECKIT_GRAPH_*` variables form a dedicated feature family (see [Section 6](#6-graph) and [Section 7](#7-graph-calibration)) controlling structural code graph indexing, graph-first routing in the search pipeline, causal graph traversal, and calibration profiles. Since graph-first routing is now the default query dispatch order (Code Graph -> CocoIndex -> Memory), the graph env vars are among the most impactful configuration levers.
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:65:3. [Search Pipeline: Core](#3-search-pipeline-core)
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:66:4. [Search Pipeline: Fusion and Scoring](#4-search-pipeline-fusion-and-scoring)
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:67:5. [Search Pipeline: Query Intelligence](#5-search-pipeline-query-intelligence)
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:94:| `SPECKIT_DYNAMIC_INIT` | `true` | boolean | Dynamic startup instruction injection for the MCP server. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:98:| `SPECKIT_SAVE_PLANNER_MODE` | `plan-only` | string | Canonical save planner mode: `plan-only` (default), `full-auto`, or `hybrid`. Since the Phase 017 H-56-1 fix, all modes still refresh packet metadata on `/memory:save`; `plan-only` no longer leaves `description.json.lastUpdated` or `graph-metadata.json` untouched. `full-auto` keeps the legacy atomic apply path; `hybrid` is reserved for future mixed flows and currently behaves the same as `plan-only`. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:100:| `SPECKIT_RECONSOLIDATION_ENABLED` | `false` | boolean | Opt-in save-time reconsolidation for planner-first flows. Disabled by default on saves. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:101:| `SPECKIT_POST_INSERT_ENRICHMENT_ENABLED` | `false` | boolean | Opt-in save-time post-insert enrichment bundle for planner-first flows. Disabled by default on saves. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:102:| `SPECKIT_QUALITY_AUTO_FIX` | `false` | boolean | Opt-in save-time quality auto-fix retries for planner-first flows. Disabled by default on saves. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:108:<!-- ANCHOR:search-pipeline-core -->
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:115:| `SPECKIT_RRF_K_EXPERIMENTAL` | `true` | boolean | Per-intent RRF K selection from the D1 K-sweep grid. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:116:| `SPECKIT_SEARCH_FALLBACK` | `true` | boolean | Quality-aware 3-tier search fallback chain (PI-A2). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:117:| `SPECKIT_COMPLEXITY_ROUTER` | `true` | boolean | Query complexity classification for routing (simple/moderate/deep). Graduated ON. | `lib/search/query-classifier.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:118:| `SPECKIT_MMR` | `true` | boolean | Graph-guided Maximal Marginal Relevance diversity reranking. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:119:| `SPECKIT_CROSS_ENCODER` | `true` | boolean | Cross-encoder reranking gate. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:120:| `SPECKIT_MULTI_QUERY` | `true` | boolean | Multi-query expansion for deep-mode retrieval. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:121:| `SPECKIT_EMBEDDING_EXPANSION` | `true` | boolean | Query expansion for embedding-based retrieval (R12). Suppressed when classification = "simple". Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:122:| `SPECKIT_CONFIDENCE_TRUNCATION` | `true` | boolean | Confidence-gap truncation for low-confidence result tails. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:123:| `SPECKIT_CHANNEL_MIN_REP` | `true` | boolean | Channel minimum-representation promotion after fusion. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:124:| `SPECKIT_DYNAMIC_TOKEN_BUDGET` | `true` | boolean | Dynamic token budget allocation by query complexity. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:125:| `SPECKIT_TRM` | `true` | boolean | Transparent Reasoning Module: evidence-gap detection. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:127:<!-- /ANCHOR:search-pipeline-core -->
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:131:<!-- ANCHOR:search-pipeline-fusion -->
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:140:| `SPECKIT_SESSION_BOOST` | `true` | boolean | Session attention boost for search result re-ranking. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:141:| `SPECKIT_CAUSAL_BOOST` | `true` | boolean | Causal graph traversal boost for search result amplification. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:142:| `SPECKIT_CALIBRATED_OVERLAP_BONUS` | `true` | boolean | Calibrated overlap bonus for multi-channel convergence (REQ-D1-001). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:143:| `SPECKIT_NEGATIVE_FEEDBACK` | `true` | boolean | Negative-feedback confidence demotion in ranking (T002b/A4). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:144:| `SPECKIT_TEMPORAL_CONTIGUITY` | `true` | boolean | Temporal contiguity boost on raw Stage 1 vector results. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:145:| `SPECKIT_RECENCY_FUSION_WEIGHT` | `0.07` | number | Weight of recency signal in Stage 2 fusion scoring. | `lib/search/pipeline/stage2-fusion.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:146:| `SPECKIT_RECENCY_FUSION_CAP` | `0.10` | number | Maximum recency contribution cap in Stage 2 fusion. | `lib/search/pipeline/stage2-fusion.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:148:| `SPECKIT_FOLDER_SCORING` | `true` | boolean | Folder-level relevance scoring. Graduated ON. | `lib/search/folder-relevance.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:150:| `SPECKIT_FOLDER_TOP_K` | `5` | number | Number of top folder-scored results to inject. | `lib/search/hybrid-search.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:151:| `SPECKIT_FOLDER_DISCOVERY` | `true` | boolean | Automatic spec folder discovery via description cache (PI-B3). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:152:<!-- /ANCHOR:search-pipeline-fusion -->
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:156:<!-- ANCHOR:search-pipeline-query -->
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:161:| `SPECKIT_QUERY_DECOMPOSITION` | `true` | boolean | Bounded facet detection for deep-mode queries: splits into up to 3 sub-queries (REQ-D2-001). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:162:| `SPECKIT_QUERY_SURROGATES` | `true` | boolean | Index-time surrogate metadata for recall improvement (REQ-D2-005). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:163:| `SPECKIT_QUERY_CONCEPT_EXPANSION` | `true` | boolean | Query concept expansion via alias matching for hybrid search (Phase B T016). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:164:| `SPECKIT_LLM_REFORMULATION` | `true` | boolean | Corpus-grounded LLM query reformulation, deep-mode only (REQ-D2-003). Requires LLM endpoint. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:165:| `SPECKIT_HYDE` | `true` | boolean | Hypothetical Document Embeddings for low-confidence deep queries (REQ-D2-004). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:166:| `SPECKIT_HYDE_ACTIVE` | (derived) | boolean | Runtime HyDE activation gate. Lowercase `true` enables. | `lib/search/hyde.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:167:| `SPECKIT_HYDE_LOG` | `false` | boolean | Enable verbose HyDE generation logging. Opt-in. | `lib/search/hyde.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:168:| `SPECKIT_INTENT_CONFIDENCE_FLOOR` | `0.25` | number | Minimum confidence for auto-detected intent. Below this, overrides to "understand". | `handlers/memory-search.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:169:| `SPECKIT_INTENT_AUTO_PROFILE` | `true` | boolean | Intent-to-profile auto-routing: auto-selects response profile from classifyIntent() results. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:170:<!-- /ANCHOR:search-pipeline-query -->
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:179:| `SPECKIT_GRAPH_UNIFIED` | `true` | boolean | Unified graph search integration. Graduated ON. Set `false` to disable all graph features. | `core/db-state.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:180:| `SPECKIT_GRAPH_SIGNALS` | `true` | boolean | Graph momentum scoring and causal depth signals (N2a+N2b). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:181:| `SPECKIT_GRAPH_WALK_ROLLOUT` | (derived) | string | Graph walk rollout state: `off`, `trace_only`, or `bounded_runtime`. Defaults to `bounded_runtime` when GRAPH_SIGNALS is ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:182:| `SPECKIT_GRAPH_WEIGHT_CAP` | `0.15` | number | Maximum graph contribution in Stage 2 scoring. | `lib/search/graph-calibration.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:183:| `SPECKIT_GRAPH_REFRESH_MODE` | `write_local` | string | Graph refresh mode: `off`, `write_local`, or `scheduled` (REQ-D3-003). | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:184:| `SPECKIT_GRAPH_LOCAL_THRESHOLD` | (internal) | number | Local graph density threshold for graph operations. | `lib/search/graph-lifecycle.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:185:| `SPECKIT_GRAPH_CONCEPT_ROUTING` | `true` | boolean | Query-time alias matching for concept routing (REQ-D2-002). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:186:| `SPECKIT_GRAPH_CONTEXT_INJECTION` | `true` | boolean | Always-on graph context injection: runs concept routing even without seed results (Phase B T020). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:187:| `SPECKIT_GRAPH_FALLBACK` | `true` | boolean | Graph-expanded fallback on zero/weak results (Phase B T017). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:188:| `SPECKIT_GRAPH_CALIBRATION_PROFILE` | `true` | boolean | Graph calibration profile enforcement and community thresholds (REQ-D3-005/006). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:189:| `SPECKIT_LLM_GRAPH_BACKFILL` | `true` | boolean | Async LLM graph backfill for high-value documents (REQ-D3-004). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:190:| `SPECKIT_COMMUNITY_DETECTION` | `true` | boolean | Community detection via BFS connected components + Louvain escalation (N2c). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:191:| `SPECKIT_COMMUNITY_SUMMARIES` | `true` | boolean | Community summary generation and search channel. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:192:| `SPECKIT_COMMUNITY_SEARCH_FALLBACK` | `true` | boolean | Community-level search as fallback channel (Phase B T018). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:193:| `SPECKIT_DUAL_RETRIEVAL` | `true` | boolean | Dual-level retrieval mode: `local` (entity), `global` (community), `auto` (local + fallback) (Phase B T019). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:194:| `SPECKIT_DEGREE_BOOST` | `true` | boolean | Causal-edge degree-based re-ranking. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:195:| `SPECKIT_TEMPORAL_EDGES` | `true` | boolean | Temporal validity tracking for causal edges (Phase D T036). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:196:| `SPECKIT_TYPED_TRAVERSAL` | `true` | boolean | Sparse-first + intent-aware typed traversal (D3 Phase A). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:197:| `SPECKIT_ENTITY_LINKING` | `true` | boolean | Cross-document entity linking (S5). Requires AUTO_ENTITIES. Graduated ON. | `lib/search/search-flags.ts`, `lib/search/graph-lifecycle.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:198:| `SPECKIT_ENTITY_LINKING_MAX_DENSITY` | `1.0` | number | Density guard threshold: skip entity linking when projected graph density exceeds this value. | `lib/search/entity-linker.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:199:| `SPECKIT_AUTO_ENTITIES` | `true` | boolean | Auto entity extraction: rule-based noun-phrase extraction at save time (R10). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:200:| `SPECKIT_RESULT_PROVENANCE` | `true` | boolean | Include graph evidence metadata (edges, communities, boost factors) in search results (Phase C T027). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:212:| `SPECKIT_CALIBRATION_PROFILE_NAME` | `default` | string | Named calibration profile: `default` or `aggressive`. | `lib/search/graph-calibration.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:213:| `SPECKIT_N2A_CAP` | (profile) | number | N2a cap for RRF fusion overflow prevention. Overrides the active calibration profile value. | `lib/search/graph-calibration.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:214:| `SPECKIT_N2B_CAP` | (profile) | number | N2b cap for RRF fusion overflow prevention. Overrides the active calibration profile value. | `lib/search/graph-calibration.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:215:| `SPECKIT_LOUVAIN_MIN_DENSITY` | (profile) | number | Minimum graph density required to activate Louvain community detection. | `lib/search/graph-calibration.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:216:| `SPECKIT_LOUVAIN_MIN_SIZE` | (profile) | number | Minimum component node count required to activate Louvain. | `lib/search/graph-calibration.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:232:| `SPECKIT_RECONSOLIDATION` | `true` | boolean | Reconsolidation-on-save for memory deduplication (TM-06). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:233:| `SPECKIT_ASSISTIVE_RECONSOLIDATION` | `true` | boolean | Assistive reconsolidation for near-duplicate detection (REQ-D4-005). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:234:| `SPECKIT_CONSOLIDATION` | `true` | boolean | Consolidation engine: contradiction scan, Hebbian strengthening, staleness detection (N3-lite). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:235:| `SPECKIT_MEMORY_SUMMARIES` | `true` | boolean | TF-IDF extractive summary generation as search channel (R8). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:236:| `SPECKIT_PRESSURE_POLICY` | `true` | boolean | Token-pressure policy for memory_context responses. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:237:| `SPECKIT_AUTO_RESUME` | `true` | boolean | Automatic session resume context injection for memory_context. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:250:| `SPECKIT_IMPLICIT_FEEDBACK_LOG` | `true` | boolean | Implicit feedback event ledger for `search_shown`, `result_cited`, `query_reformulated`, `same_topic_requery`, and `follow_on_tool_use`. Event logging only, with no ranking side effects (REQ-D4-001). Graduated ON. | `lib/feedback/feedback-ledger.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:252:| `SPECKIT_SHADOW_LEARNING` | `false` | boolean | Shadow learned model loading for Stage 2 weight combiner. Opt-in: set `true` to enable. | `lib/search/pipeline/stage2-fusion.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:253:| `SPECKIT_LEARNED_STAGE2_COMBINER` | `true` | boolean | Learned Stage 2 weight combiner in shadow mode (REQ-D1-006). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:254:| `SPECKIT_LEARNED_STAGE2_MODEL` | (auto) | string | Custom file path for the learned Stage 2 model. Absolute or relative to cwd. | `lib/search/pipeline/stage2-fusion.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:255:| `SPECKIT_BATCH_LEARNED_FEEDBACK` | `true` | boolean | Weekly batch feedback learning pipeline (REQ-D4-004). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:258:| `SPECKIT_USAGE_RANKING` | `true` | boolean | Usage-weighted ranking signal (Phase D T036). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:260:| `SPECKIT_SAVE_QUALITY_GATE` | `true` | boolean | Pre-storage quality gate for memory saves. Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:261:| `SPECKIT_SAVE_QUALITY_GATE_EXCEPTIONS` | `true` | boolean | Short-critical quality gate exception for decision context types (REQ-D4-003). Graduated ON. | `lib/search/search-flags.ts`, `lib/validation/save-quality-gate.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:262:| `SPECKIT_QUALITY_LOOP` | `true` | boolean | Verify-fix-verify memory quality loop (T008). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:285:| `SPECKIT_CONTEXT_HEADERS` | `true` | boolean | Contextual tree headers for Stage 4 result enrichment (P1-4). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:286:| `SPECKIT_PROGRESSIVE_DISCLOSURE_V1` | `true` | boolean | Progressive disclosure: summary layer + snippet + cursor pagination (REQ-D5-005). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:287:| `SPECKIT_SESSION_RETRIEVAL_STATE_V1` | `true` | boolean | Cross-turn retrieval session state for dedup and goal-aware refinement (REQ-D5-006). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:288:| `SPECKIT_EMPTY_RESULT_RECOVERY_V1` | `true` | boolean | Empty/weak result recovery UX with diagnostic payload (REQ-D5-001). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:289:| `SPECKIT_RESULT_CONFIDENCE_V1` | `true` | boolean | Per-result calibrated confidence scoring (REQ-D5-004). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:290:| `SPECKIT_RESULT_EXPLAIN_V1` | `true` | boolean | Two-tier result explainability (REQ-D5-002). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:291:| `SPECKIT_RESULT_EXPLAIN_DEBUG` | `false` | boolean | Detailed debug-level result explainability. Opt-in: set `true` to enable. | `formatters/search-results.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:292:| `SPECKIT_RESPONSE_PROFILE_V1` | `true` | boolean | Mode-aware response profile formatting (REQ-D5-003). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:293:| `SPECKIT_RESPONSE_TRACE` | `false` | boolean | Include full retrieval trace in search responses. Opt-in: set `true` to enable. | `handlers/memory-search.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:326:| `SPECKIT_ENCODING_INTENT` | `true` | boolean | Encoding-intent capture at index time (R16). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:327:| `SPECKIT_ONTOLOGY_HOOKS` | `true` | boolean | Ontology-guided extraction validation hooks (Phase D T036). Graduated ON. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:329:| `SPECKIT_EXTRACTION` | `true` | boolean | Entity/relation extraction pipeline. Graduated ON. | `lib/search/search-flags.ts` (via tests) |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:330:| `SPECKIT_FILE_WATCHER` | `false` | boolean | Real-time file watcher for markdown reindexing (P1-7). **Default OFF**: opt-in. Honors ROLLOUT_PERCENT. | `lib/search/search-flags.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:342:| `SPECKIT_RERANKER_MODEL` | (auto) | string | Custom GGUF model path for local reranker. | `lib/search/local-reranker.ts` |
.opencode/skills/system-spec-kit/mcp_server/ENV_REFERENCE.md:343:| `SPECKIT_RERANKER_TIMEOUT_MS` | `30000` | number | Timeout in milliseconds for reranker model inference. | `lib/search/local-reranker.ts` |
.opencode/skills/mcp-coco-index/mcp_server/pyproject.toml:17:keywords = ["cocoindex", "codebase", "indexing", "mcp", "vector-search"]
.opencode/skills/mcp-coco-index/SKILL.md:3:description: "Semantic code search via vector embeddings. CocoIndex Code enables natural-language discovery of relevant code, patterns, and implementations. CLI for direct use; MCP exposes a single `search` tool for AI agent integration."
.opencode/skills/mcp-coco-index/SKILL.md:8:<!-- Keywords: cocoindex-code, semantic-search, vector-embeddings, code-search, mcp-server, ccc, codebase-indexing, voyage-code-3, all-MiniLM-L6-v2 -->
.opencode/skills/mcp-coco-index/SKILL.md:10:# CocoIndex Code - Semantic Code Search via Vector Embeddings
.opencode/skills/mcp-coco-index/SKILL.md:12:Natural language code search through two complementary approaches: CLI (ccc) for speed and one-off queries, MCP server (1 tool: `search`) for AI agent integration via stdio transport.
.opencode/skills/mcp-coco-index/SKILL.md:18:> **Forked From**: This skill bundles a soft-fork of [cocoindex-code](https://github.com/cocoindex-io/cocoindex-code) (Apache 2.0). Upstream version forked: 0.2.3. Current fork version: 0.2.3+spec-kit-fork.0.2.0. Patches: REQ-001..006 (mirror dedup + path-class reranking) from the spec packet at `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/011-mcp-runtime-stress-remediation/004-cocoindex-overfetch-dedup-rerank/` (currently numbered `004`; tracked as `009` during research and in commit history). See NOTICE and changelog/CHANGELOG.md for the full attribution and modification list.
.opencode/skills/mcp-coco-index/SKILL.md:23:- User asks to "find code that does X" or "search for implementations of Y"
.opencode/skills/mcp-coco-index/SKILL.md:27:- User mentions "semantic search", "code search", "find similar code"
.opencode/skills/mcp-coco-index/SKILL.md:37:- "semantic search", "find code that", "search for implementations"
.opencode/skills/mcp-coco-index/SKILL.md:39:- "cocoindex", "ccc", "vector search"
.opencode/skills/mcp-coco-index/SKILL.md:40:- "find similar", "code search", "search codebase"
.opencode/skills/mcp-coco-index/SKILL.md:48:- Exact text or regex search (use Grep instead)
.opencode/skills/mcp-coco-index/SKILL.md:49:- File name or path search (use Glob instead)
.opencode/skills/mcp-coco-index/SKILL.md:53:- Non-code files (semantic search is optimized for source code)
.opencode/skills/mcp-coco-index/SKILL.md:66:| CONDITIONAL | If intent signals match  | references/search_patterns.md, references/cross_cli_playbook.md |
.opencode/skills/mcp-coco-index/SKILL.md:81:    "SEARCH": {"weight": 4, "keywords": ["search", "find", "where", "similar", "semantic", "code that"]},
.opencode/skills/mcp-coco-index/SKILL.md:91:    "SEARCH": ["references/search_patterns.md", "references/cross_cli_playbook.md", "references/tool_reference.md"],
.opencode/skills/mcp-coco-index/SKILL.md:95:    "TROUBLESHOOT": ["references/tool_reference.md", "references/cross_cli_playbook.md", "references/search_patterns.md"],
.opencode/skills/mcp-coco-index/SKILL.md:102:    "ON_DEMAND_KEYWORDS": ["full troubleshooting", "all commands", "configuration guide", "cross cli playbook", "semantic code search", "semantic search", "vector-search blending", "before grep", "find code that"],
.opencode/skills/mcp-coco-index/SKILL.md:103:    "ON_DEMAND": ["references/tool_reference.md", "references/search_patterns.md", "references/cross_cli_playbook.md"],
.opencode/skills/mcp-coco-index/SKILL.md:189:CocoIndex Code provides two access patterns for semantic code search:
.opencode/skills/mcp-coco-index/SKILL.md:191:1. **CLI (ccc)** - Direct terminal usage, fastest for one-off searches
.opencode/skills/mcp-coco-index/SKILL.md:194:### CLI Approach (Primary) - CocoIndex Code CLI
.opencode/skills/mcp-coco-index/SKILL.md:199:# Basic semantic search
.opencode/skills/mcp-coco-index/SKILL.md:200:ccc search "error handling middleware" --limit 5
.opencode/skills/mcp-coco-index/SKILL.md:203:ccc search "database connection" --lang typescript
.opencode/skills/mcp-coco-index/SKILL.md:206:ccc search "authentication" --path "src/**"
.opencode/skills/mcp-coco-index/SKILL.md:209:ccc search "retry logic" --lang python --path "lib/**" --limit 10
.opencode/skills/mcp-coco-index/SKILL.md:239:The MCP server exposes **1 tool only**: `search`. The `status`, `index`, and `reset` operations are CLI-only commands and are NOT available as MCP tools.
.opencode/skills/mcp-coco-index/SKILL.md:243:| `search` | Semantic search across codebase | `query` (str, required), `languages` (list\|null), `paths` (list\|null), `limit` (int, default 5), `offset` (int, default 0), `refresh_index` (bool, default True) |
.opencode/skills/mcp-coco-index/SKILL.md:247:CocoIndex Code supports two embedding models, configured via `~/.cocoindex_code/global_settings.yml`:
.opencode/skills/mcp-coco-index/SKILL.md:251:| `voyage/voyage-code-3` (primary) | Cloud via LiteLLM | 1024 | `VOYAGE_API_KEY` required | Higher quality code search |
.opencode/skills/mcp-coco-index/SKILL.md:260:CocoIndex Code resolves the project root in this order:
.opencode/skills/mcp-coco-index/SKILL.md:269:The CocoIndex Code daemon manages background indexing and serves search requests:
.opencode/skills/mcp-coco-index/SKILL.md:301:       +-- Indexes for fast approximate nearest neighbor search
.opencode/skills/mcp-coco-index/SKILL.md:319:Scores above 0.5 typically indicate strong semantic relevance. Always verify results with the Read tool since semantic search can surface false positives.
.opencode/skills/mcp-coco-index/SKILL.md:321:> **Fork-specific telemetry (skill bundles a soft-fork at `0.2.3+spec-kit-fork.0.2.0`).** Result rows carry seven additional fields that vanilla upstream cocoindex-code does NOT emit: `source_realpath` and `content_hash` (canonical chunk identity), `path_class` (taxonomy: implementation / tests / docs / spec_research / generated / vendor), `dedupedAliases` and `uniqueResultCount` (mirror-folder dedup signals), `raw_score` (pre-rerank score, preserved for audit), and `rankingSignals` (per-result rerank breakdown). Implementation-intent queries get a bounded `±0.05` rerank toward `path_class == implementation`. Full schema, types, examples, and reading guidance live in [`references/tool_reference.md` §7 Fork-Specific Output Telemetry](references/tool_reference.md#-7-fork-specific-output-telemetry); the canonical field-to-REQ mapping lives in [`changelog/CHANGELOG.md`](changelog/CHANGELOG.md).
.opencode/skills/mcp-coco-index/SKILL.md:333:1. **ALWAYS check index status before searching**
.opencode/skills/mcp-coco-index/SKILL.md:334:   - Run `ccc status` before the first search in a session
.opencode/skills/mcp-coco-index/SKILL.md:345:4. **ALWAYS verify search results with the Read tool**
.opencode/skills/mcp-coco-index/SKILL.md:346:   - Semantic search can return false positives
.opencode/skills/mcp-coco-index/SKILL.md:378:When sending multiple searches in sequence (e.g., exploring a codebase):
.opencode/skills/mcp-coco-index/SKILL.md:387:1. **NEVER assume semantic search is 100% accurate**
.opencode/skills/mcp-coco-index/SKILL.md:395:3. **NEVER use semantic search for exact string matching**
.opencode/skills/mcp-coco-index/SKILL.md:397:   - Semantic search is for conceptual or intent-based queries
.opencode/skills/mcp-coco-index/SKILL.md:399:4. **NEVER skip the index status check before first search**
.opencode/skills/mcp-coco-index/SKILL.md:415:2. **ESCALATE IF search returns no results for reasonable queries**
.opencode/skills/mcp-coco-index/SKILL.md:430:   - Suggest combining semantic search with Grep for better coverage
.opencode/skills/mcp-coco-index/SKILL.md:449:ccc search "query text"                    # Basic search
.opencode/skills/mcp-coco-index/SKILL.md:450:ccc search "query" --limit 10             # Limit results
.opencode/skills/mcp-coco-index/SKILL.md:451:ccc search "query" --lang typescript      # Filter by language
.opencode/skills/mcp-coco-index/SKILL.md:452:ccc search "query" --path "src/**"        # Filter by path
.opencode/skills/mcp-coco-index/SKILL.md:466:The CocoIndex MCP server exposes `search` as its primary tool. Additionally, 3 management tools are available via the Spec Kit Memory MCP server's code graph module:
.opencode/skills/mcp-coco-index/SKILL.md:470:| `search` | CocoIndex | Semantic search across code    | `query` (str), `languages` (list\|null), `paths` (list\|null), `limit` (int, default 5), `offset` (int, default 0), `refresh_index` (bool, default true) |
.opencode/skills/mcp-coco-index/SKILL.md:471:| `ccc_status` | Spec Kit Memory | Check CocoIndex availability and index stats | none |
.opencode/skills/mcp-coco-index/SKILL.md:473:| `ccc_feedback` | Spec Kit Memory | Submit search result quality feedback | `query` (str), `rating` (helpful\|not_helpful\|partial), `comment` (str, optional) |
.opencode/skills/mcp-coco-index/SKILL.md:477:> **Companion recovery surface**: In the integrated Spec Kit workflow, use `/spec_kit:resume` first. Recover packet context in the order `handover.md -> _memory.continuity -> spec docs`, then use CocoIndex when those canonical packet sources no longer answer the question.
.opencode/skills/mcp-coco-index/SKILL.md:481:CocoIndex Code supports 28+ languages with language-aware chunk splitting:
.opencode/skills/mcp-coco-index/SKILL.md:512:        YES --> Use ccc search
.opencode/skills/mcp-coco-index/SKILL.md:556:Semantic search fills the gap between exact pattern matching and conceptual code discovery:
.opencode/skills/mcp-coco-index/SKILL.md:561:| Glob   | File names, path patterns       | Cannot search file contents         |
.opencode/skills/mcp-coco-index/SKILL.md:562:| ccc    | Intent-based, conceptual search | Approximate - needs verification    |
.opencode/skills/mcp-coco-index/SKILL.md:566:# Step 1: Semantic search to find candidate files
.opencode/skills/mcp-coco-index/SKILL.md:567:ccc search "rate limiting middleware" --lang typescript --limit 5
.opencode/skills/mcp-coco-index/SKILL.md:579:- CocoIndex Code handles code search; Code Mode handles external APIs
.opencode/skills/mcp-coco-index/SKILL.md:587:**Read**: Verify search results by reading matched files
.opencode/skills/mcp-coco-index/SKILL.md:588:**Grep**: Confirm exact patterns after semantic search narrows candidates
.opencode/skills/mcp-coco-index/SKILL.md:589:**Glob**: Locate files by name when semantic search identifies a module
.opencode/skills/mcp-coco-index/SKILL.md:593:**CocoIndex Code (ccc)**:
.opencode/skills/mcp-coco-index/SKILL.md:596:- Purpose: Semantic code search via vector embeddings
.opencode/skills/mcp-coco-index/SKILL.md:609:| **install.sh** | Install CocoIndex  | `bash .opencode/skills/mcp-coco-index/scripts/install.sh`                  |
.opencode/skills/mcp-coco-index/SKILL.md:619:| **search_patterns.md**      | Search query patterns    | Effective query formulation and filter usage |
.opencode/skills/mcp-coco-index/SKILL.md:620:| **cross_cli_playbook.md**   | Cross-CLI usage recipe   | Safe defaults for repeated searches and troubleshooting |
.opencode/skills/mcp-coco-index/README.md:2:title: "CocoIndex Code - Semantic Code Search"
.opencode/skills/mcp-coco-index/README.md:3:description: "Semantic code search via vector embeddings. CocoIndex Code enables natural-language discovery of code, patterns, and implementations across 28+ languages using a CLI and a single MCP search tool."
.opencode/skills/mcp-coco-index/README.md:5:  - "semantic search"
.opencode/skills/mcp-coco-index/README.md:9:  - "code search"
.opencode/skills/mcp-coco-index/README.md:10:  - "vector search"
.opencode/skills/mcp-coco-index/README.md:14:# CocoIndex Code - Semantic Code Search
.opencode/skills/mcp-coco-index/README.md:33:Patches landed per the spec packet at `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/011-mcp-runtime-stress-remediation/004-cocoindex-overfetch-dedup-rerank/` (the cocoindex-overfetch-dedup packet — currently numbered `004` in the renumbered phase tree, tracked as `009` during research and in commit history such as `1b62e976d`): mirror-folder duplicate suppression, canonical path identity, path-class reranking for implementation-intent queries, and ranking telemetry.
.opencode/skills/mcp-coco-index/README.md:61:CocoIndex Code is a semantic code search tool built on vector embeddings. Where `grep` matches exact characters, CocoIndex Code matches meaning. Ask for "retry logic with exponential backoff" and it returns code that implements that pattern, regardless of how the author named variables or functions. This makes it the right tool when you know what a piece of code does but not where it lives or what it is called.
.opencode/skills/mcp-coco-index/README.md:63:The skill ships with two access modes. The CLI (`ccc`) is fastest for one-off queries and all index management operations. The MCP server (`ccc mcp`) exposes a single `search` tool that AI agents call directly via stdio transport, integrating semantic search into any tool-calling workflow without leaving the conversation.
.opencode/skills/mcp-coco-index/README.md:74:| MCP tools exposed | 1 (`search`) |
.opencode/skills/mcp-coco-index/README.md:86:| `ccc search` (CocoIndex) | You know what code does but not where it lives | Approximate, needs verification |
.opencode/skills/mcp-coco-index/README.md:87:| `code_graph_query` | You need exact callers, imports, or structural dependencies | Requires the structural graph to be indexed first |
.opencode/skills/mcp-coco-index/README.md:89:| `Glob` | You know the file name or extension pattern | Cannot search file contents |
.opencode/skills/mcp-coco-index/README.md:90:| `Read` | You know the exact file path | No search capability |
.opencode/skills/mcp-coco-index/README.md:96:| Semantic search | Query by concept or intent, not exact text |
.opencode/skills/mcp-coco-index/README.md:106:In the broader system-spec-kit stack, CocoIndex is the semantic half of a three-system retrieval model: CocoIndex finds conceptually similar code, Code Graph answers structural questions, and session bootstrap surfaces CocoIndex readiness during recovery. The companion lifecycle helpers exposed through system-spec-kit are `ccc_status`, `ccc_reindex`, and `ccc_feedback`.
.opencode/skills/mcp-coco-index/README.md:133:Confirm files are indexed before searching.
.opencode/skills/mcp-coco-index/README.md:144:ccc search "authentication middleware"
.opencode/skills/mcp-coco-index/README.md:145:ccc search "error handling" --lang typescript
.opencode/skills/mcp-coco-index/README.md:146:ccc search "database migration" --path "src/**" --limit 5
.opencode/skills/mcp-coco-index/README.md:158:CocoIndex Code resolves queries by embedding the natural-language query text and comparing the resulting vector against pre-computed vectors for every code chunk in the index. This means the search engine reads intent, not characters. A query for "graceful shutdown handler" finds code that tears down servers or releases resources, even if the words "graceful", "shutdown", or "handler" never appear in that code.
.opencode/skills/mcp-coco-index/README.md:164:The CLI and MCP interfaces are complementary, not redundant. The CLI handles index management operations (`index`, `status`, `reset`, `init`, `daemon`) that have no MCP equivalents. The MCP server exposes only the `search` tool because index management is a human-initiated operation, not an agent-initiated one. When building an AI workflow that needs semantic search, configure the MCP server and let agents call `search` directly.
.opencode/skills/mcp-coco-index/README.md:172:| `ccc search QUERY` | Semantic search | `--lang`, `--path`, `--limit`, `--offset`, `--refresh` |
.opencode/skills/mcp-coco-index/README.md:182:**MCP tool: `search`**
.opencode/skills/mcp-coco-index/README.md:186:| `query` | string | Yes | - | Natural-language search query |
.opencode/skills/mcp-coco-index/README.md:191:| `refresh_index` | boolean | No | true | Trigger index refresh before searching |
.opencode/skills/mcp-coco-index/README.md:208:| `voyage/voyage-code-3` | Cloud via LiteLLM | 1024 | `VOYAGE_API_KEY` | Higher quality code search |
.opencode/skills/mcp-coco-index/README.md:234:    01--core-cli-commands/         Test cases for search, index, status, init, reset
.opencode/skills/mcp-coco-index/README.md:235:    02--mcp-search-tool/           Test cases for MCP search tool
.opencode/skills/mcp-coco-index/README.md:240:    search_patterns.md             Query writing strategies and filter examples
.opencode/skills/mcp-coco-index/README.md:244:    install.sh                     Install CocoIndex Code into skill venv
.opencode/skills/mcp-coco-index/README.md:312:Set `"disabled": false` to activate. The MCP server is disabled by default to avoid adding search context to sessions that do not need it.
.opencode/skills/mcp-coco-index/README.md:324:CocoIndex Code resolves the project root in this order:
.opencode/skills/mcp-coco-index/README.md:347:**Example 1: Concept search with filters**
.opencode/skills/mcp-coco-index/README.md:352:# Broad search first
.opencode/skills/mcp-coco-index/README.md:353:ccc search "error handling and recovery"
.opencode/skills/mcp-coco-index/README.md:356:ccc search "error handling and recovery" --lang typescript
.opencode/skills/mcp-coco-index/README.md:359:ccc search "error handling and recovery" --lang typescript --path "src/api/" --limit 5
.opencode/skills/mcp-coco-index/README.md:364:Use semantic search to find candidate files, then verify with Grep and Read.
.opencode/skills/mcp-coco-index/README.md:367:# Step 1: Semantic search finds candidate files
.opencode/skills/mcp-coco-index/README.md:368:ccc search "rate limiting middleware" --lang typescript --limit 5
.opencode/skills/mcp-coco-index/README.md:379:An AI agent calls the MCP `search` tool directly. Set `refresh_index` to `false` on follow-up queries within the same session.
.opencode/skills/mcp-coco-index/README.md:413:**Empty search results for reasonable queries**
.opencode/skills/mcp-coco-index/README.md:415:What you see: `ccc search "authentication middleware"` returns zero results or only low-score matches.
.opencode/skills/mcp-coco-index/README.md:432:What you see: MCP search tool returns a `ComponentContext` error when multiple queries fire with `refresh_index=true` at the same time.
.opencode/skills/mcp-coco-index/README.md:478:Common causes: CocoIndex Code requires Python 3.11 or later. The system Python may be an older version.
.opencode/skills/mcp-coco-index/README.md:494:**Q: Why does CocoIndex Code only expose one MCP tool when the CLI has seven commands?**
.opencode/skills/mcp-coco-index/README.md:496:A: Index management operations (`index`, `status`, `reset`, `init`, `daemon`) are intended for human-initiated workflows, not agent-initiated ones. An agent asking to reset a codebase index would be a destructive action with no confirmation step. The MCP interface exposes only `search` to keep agent behavior predictable and safe. Run index management commands from a terminal.
.opencode/skills/mcp-coco-index/README.md:502:A: Use Voyage Code 3 when search quality matters more than avoiding an API dependency. The local model (`all-MiniLM-L6-v2`) is a general-purpose sentence embedding model with 384 dimensions. It works well for most queries but can miss nuanced code patterns. Voyage Code 3 was trained on code and produces 1024-dimensional vectors, giving it better discrimination between semantically similar but functionally different patterns. Switch to it when you notice too many false positives or misses on important queries. Remember: switching models requires `ccc reset && ccc index`.
.opencode/skills/mcp-coco-index/README.md:530:| [references/search_patterns.md](references/search_patterns.md) | Query writing strategies and filter examples |
.opencode/skills/mcp-coco-index/README.md:534:| [scripts/install.sh](scripts/install.sh) | Install CocoIndex Code |
.opencode/skills/mcp-coco-index/README.md:542:| [system-spec-kit](../system-spec-kit/SKILL.md) | Context preservation and memory | Complementary: semantic memory vs. semantic code search |
.opencode/skills/mcp-coco-index/README.md:549:| CocoIndex GitHub | https://github.com/cocoindex-io/cocoindex |
.opencode/skills/mcp-coco-index/README.md:550:| CocoIndex Code on PyPI | https://pypi.org/project/cocoindex-code/ |
.opencode/skills/mcp-coco-index/scripts/update.sh:27:echo "=== CocoIndex upstream-sync helper ==="
.opencode/skills/mcp-coco-index/scripts/update.sh:101:REQ-004 — indexer.py + schema.py: path_class taxonomy (implementation/tests/docs/spec_research/generated/vendor)
.opencode/skills/mcp-coco-index/scripts/update.sh:102:REQ-005 — query.py: bounded reranking +0.05 implementation, -0.05 docs/spec_research for implementation-intent queries
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/__init__.py:1:"""CocoIndex Code - MCP server for indexing and querying codebases."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/indexer.py:1:"""CocoIndex app for indexing codebases."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/indexer.py:71:            "research" in specs_tail
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/indexer.py:72:            or name == "research.md"
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/indexer.py:75:            return "spec_research"
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/settings.py:93:# CocoIndex context key for project settings
.opencode/skills/mcp-coco-index/assets/config_templates.md:2:title: CocoIndex Code Configuration Templates
.opencode/skills/mcp-coco-index/assets/config_templates.md:3:description: Repo-portable MCP configuration snippets for the checked-in CocoIndex integration across supported CLIs.
.opencode/skills/mcp-coco-index/assets/config_templates.md:12:# CocoIndex Code Configuration Templates
.opencode/skills/mcp-coco-index/assets/config_templates.md:14:Repo-portable MCP configuration snippets for the current checked-in CocoIndex setup.
.opencode/skills/mcp-coco-index/assets/config_templates.md:27:- MCP exposes only `search`
.opencode/skills/mcp-coco-index/assets/config_templates.md:167:- Codex runtime agents resolve through `.codex/agents/*.toml`, but the CocoIndex MCP server itself is still configured in `.codex/config.toml`
.opencode/skills/mcp-coco-index/NOTICE:20:  - REQ-004: Added path_class field with implementation/tests/docs/spec_research/generated/vendor taxonomy
.opencode/skills/mcp-coco-index/NOTICE:21:  - REQ-005: Bounded path-class reranking (+0.05 implementation, -0.05 docs/spec_research) for implementation-intent queries
.opencode/skills/mcp-coco-index/NOTICE:25:  Acceptance probe note: In the Codex sandbox, `ccc index` and `ccc search` could not
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/client.py:96:    def search(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/client.py:128:                raise RuntimeError("Connection to daemon lost during search")
.opencode/skills/mcp-coco-index/scripts/doctor.sh:5:# Read-only health check for the CocoIndex skill installation.
.opencode/skills/mcp-coco-index/scripts/doctor.sh:12:#   20 - Repo-local CocoIndex binary missing
.opencode/skills/mcp-coco-index/scripts/doctor.sh:147:printf '%s\n' "=== CocoIndex Doctor ==="
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:5:Complete installation and configuration guide for the Spec Kit Memory MCP server. This guide enables AI-powered context retrieval and conversation memory across your project. The system indexes markdown documentation from spec folders and constitutional rules to surface relevant information during AI interactions. It provides 51 tools (canonical source: `TOOL_DEFINITIONS.length` in `mcp_server/tool-schemas.ts`) covering semantic search, trigger-based memory surfacing, intent-aware context loading, causal relationship tracking, session learning, evaluation, validation, and bounded structural code-graph indexing.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:22:4. Verify the installation with a test search query
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:35:- Test semantic search with a sample query
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:77:│  Context indexing    Semantic search    Trigger matching        │
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:106:- Server starts but search returns empty or stale results
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:128:- `code_graph_query` and `code_graph_context` may repair small stale deltas inline
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:130:- successful `code_graph_context` responses include `metadata.partialOutput` and `graphMetadata.detectorProvenance` so you can tell whether the response was partial and which persisted graph metadata backed it
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:206:- `sqlite-vec` (vector extension for semantic search)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:430:- `memory_context` (unified context retrieval)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:431:- `memory_search` (semantic search)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:432:- `memory_match_triggers` (fast trigger matching)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:437:- `code_graph_query` (structural relationship queries)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:439:- `code_graph_context` (LLM-oriented graph neighborhoods)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:460:- successful `code_graph_context` responses include `metadata.partialOutput` and `graphMetadata.detectorProvenance`
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:503:  Run `code_graph_query({ operation: "blast_radius", subject: "<known-symbol-or-file>",
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:534:  .opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts \
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:540:  .opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:549:PASS criterion: source grep finds the additive badge interface and formatter wiring; static diff shows no schema or decay-logic changes in the protected files; targeted Vitest exits 0; `memory_search` results carry `confidence`, `extractionAge`, `lastAccessAge`, `orphan`, `weightHistoryChanged` on each `MemoryResultEnvelope`, preserved through `quick`/`research`/`resume` profiles.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:557:- [ ] `memory_search()` returns results (or empty if no memories are indexed yet)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:622:### memory_context: Unified Context Retrieval
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:624:`memory_context()` is the primary entry point for context loading. It detects task intent and routes to the optimal retrieval strategy automatically.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:629:- `deep`: Full semantic search with query expansion
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:640:### memory_search: Semantic Search
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:642:`memory_search()` runs vector-based similarity search across all indexed memories.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:645:- `query`: Natural language search query
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:651:### memory_match_triggers: Fast Keyword Lookup
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:653:`memory_match_triggers()` provides sub-50ms keyword-based matching. Use it for immediate context surfacing at the start of a conversation.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:712:Routes retrieval requests through per-type strategies based on the artifact being queried. Supports 8 artifact types: `spec`, `plan`, `checklist`, `decision-record`, `memory`, `implementation-summary`, `research` and `handover`. Each type applies its own indexing and ranking rules (for example, `memory` uses recency-weighted scoring while `decision-record` boosts causal edges).
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:721:- `ContextEnvelope`: Wraps all `memory_context()` responses with metadata (mode used, memories returned, intent detected)
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:722:- `RetrievalTrace`: Attached to search results, records which retrieval path was taken and why
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:784:1. AI calls `memory_context({ input: "add user profiles", mode: "auto" })`
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:883:| `code_graph_query` reports `full_scan`, or `code_graph_context` / `code_graph_query` returns `status: "blocked"` with `requiredAction: "code_graph_scan"` | The graph is empty or too stale for bounded read-path repair | Run `code_graph_scan`, then retry the structural read |
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:999:`code_graph_context` can refuse broad repair on the read path. In that case it returns `status: "blocked"` with `requiredAction: "code_graph_scan"` and `blockReason: "full_scan_required"` instead of attempting a full scan inline. Successful context responses still include `readiness`, `trustState`, `graphMetadata.detectorProvenance`, and `metadata.partialOutput`, which is the operator-facing signal that budget or deadline limits trimmed sections or anchors.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1070:This calls `memory_index_scan({ force: true })` to repopulate the search index from the restored database.
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1088:| `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-impl.ts` | Vector index implementation |
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1147:MCP TOOLS: memory_context, memory_search, memory_match_triggers,
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1163:| v1.7.x | 2026-02-20 | Cross-encoder reranking enabled by default. Co-activation score boost fix. Query expansion on deep mode. Evidence gap warnings. MMR reranking with intent-mapped lambda. Phase system support (recursive validation, phase detection scoring). Feature flag updates. `memory_context` tokenUsage parameter. 28-tool surface area. |
.opencode/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md:1164:| v1.x | 2025 | Adaptive fusion, extended telemetry, artifact-class routing, append-only mutation ledger, typed retrieval contracts. Semantic search, trigger matching, intent-aware context, session deduplication. |
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:28:    help="CocoIndex Code — index and search codebases.",
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:136:def print_search_results(response: SearchResponse) -> None:
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:137:    """Print formatted search results."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:204:def _search_with_wait_spinner(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:213:    """Run search, showing a spinner if waiting for load-time indexing."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:228:        resp = client.search(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:241:_GITIGNORE_COMMENT = "# CocoIndex Code (ccc)"
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:351:def search(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:357:    refresh: bool = _typer.Option(False, "--refresh", help="Refresh index before searching"),
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:359:    """Semantic search across the codebase."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:363:    # Refresh index with progress display before searching
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:376:    resp = _search_with_wait_spinner(
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py:385:    print_search_results(resp)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/graph-metadata.json:8:      { "target": "mcp-coco-index", "weight": 0.7, "context": "semantic search routing and discovery signals" }
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/graph-metadata.json:17:      { "target": "mcp-coco-index", "weight": 0.7, "context": "routes semantic code search requests" },
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/graph-metadata.json:24:      { "target": "sk-deep-research", "weight": 0.7, "context": "routes autonomous research requests" },
.opencode/skills/mcp-coco-index/scripts/install.sh:3:# ║ CocoIndex Code MCP Installer                                            ║
.opencode/skills/mcp-coco-index/scripts/install.sh:5:# Install the spec-kit CocoIndex Code soft-fork into the skill folder venv.
.opencode/skills/mcp-coco-index/scripts/install.sh:74:    echo "  Initializing CocoIndex Code project..."
.opencode/skills/mcp-coco-index/scripts/install.sh:98:echo "=== CocoIndex Code MCP Install Script ==="
.opencode/skills/mcp-coco-index/scripts/install.sh:125:echo "Installing CocoIndex Code MCP server..."
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/protocol.py:21:class SearchRequest(_msgspec.Struct, tag="search"):
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/protocol.py:107:class SearchResponse(_msgspec.Struct, tag="search"):
.opencode/skills/system-spec-kit/mcp_server/README.md:3:description: "Model Context Protocol server providing semantic memory, hybrid search and graph intelligence for AI-assisted development across sessions, models and tools."
.opencode/skills/system-spec-kit/mcp_server/README.md:7:  - "hybrid search"
.opencode/skills/system-spec-kit/mcp_server/README.md:9:  - "memory_context"
.opencode/skills/system-spec-kit/mcp_server/README.md:10:  - "memory_search"
.opencode/skills/system-spec-kit/mcp_server/README.md:59:| **MCP tools** | Live registry | Core memory layers plus dedicated code graph, CocoIndex dispatch, and Skill Advisor groups |
.opencode/skills/system-spec-kit/mcp_server/README.md:60:| **Search channels** | 5 core + CocoIndex bridge | Vector, FTS5, BM25, Causal Graph, Degree (+ CocoIndex semantic code search as external bridge) |
.opencode/skills/system-spec-kit/mcp_server/README.md:73:| **Search** | Vector similarity only | 5 core channels + CocoIndex bridge, fused with Reciprocal Rank Fusion (K tuned per intent) |
.opencode/skills/system-spec-kit/mcp_server/README.md:74:| **Routing** | No routing | Graph-first structural routing: Code Graph -> CocoIndex -> Memory; 3-tier FTS fallback when graph/semantic miss |
.opencode/skills/system-spec-kit/mcp_server/README.md:89:The indexed-continuity store exposes its MCP tools through 4 memory slash commands plus the borrowed recovery workflow in `/spec_kit:resume`. Dedicated code-graph, CocoIndex, and Skill Advisor tools live in the same server. Think of commands as doors into the system. Each door opens access only to the tools it needs.
.opencode/skills/system-spec-kit/mcp_server/README.md:93:| `/memory:search` | Search, retrieve and analyze knowledge | 13 tools |
.opencode/skills/system-spec-kit/mcp_server/README.md:218:  "tool": "memory_context",
.opencode/skills/system-spec-kit/mcp_server/README.md:226:The system reads your question, figures out you are looking for a past decision and routes to the right search strategy automatically.
.opencode/skills/system-spec-kit/mcp_server/README.md:243:When you search for something, the system checks several sources at once. Think of a librarian who checks the card catalog, the shelf labels, the reading room sign-out sheet and the recommendation board all at the same time.
.opencode/skills/system-spec-kit/mcp_server/README.md:245:**Five core search channels** work together, with **CocoIndex** available as an external semantic code search bridge:
.opencode/skills/system-spec-kit/mcp_server/README.md:250:| **FTS5** | Full-text search on exact words and phrases | Looking up specific terms or error messages |
.opencode/skills/system-spec-kit/mcp_server/README.md:251:| **BM25** | Keyword relevance scoring (like a search engine) | Ranking results when you know roughly what you want |
.opencode/skills/system-spec-kit/mcp_server/README.md:254:| **CocoIndex** *(bridge)* | Semantic code search via vector embeddings across source files | Finding code implementations when memory channels miss; concept-first code discovery |
.opencode/skills/system-spec-kit/mcp_server/README.md:256:**Graph-first routing** determines query dispatch order: structural queries route to the Code Graph first, then CocoIndex for semantic code discovery, then the 5-channel memory pipeline. This avoids forcing one search system to handle both structural relationships and semantic similarity.
.opencode/skills/system-spec-kit/mcp_server/README.md:266:| Tier 1 | FTS5 full-text search | Graph and semantic channels return weak results |
.opencode/skills/system-spec-kit/mcp_server/README.md:267:| Tier 2 | BM25 keyword scoring | FTS5 results below confidence floor |
.opencode/skills/system-spec-kit/mcp_server/README.md:268:| Tier 3 | Grep/Glob filesystem search | Still poor results after BM25 |
.opencode/skills/system-spec-kit/mcp_server/README.md:272:**Evidence gap detection** (TRM Z-score) flags when retrieved memories do not adequately cover the query and suggests broadening the search.
.opencode/skills/system-spec-kit/mcp_server/README.md:276:**Tool-level TTL cache** remembers recent results for 60 seconds. When you save, update or delete a spec-doc record, the cache for affected searches clears automatically. You never see stale results.
.opencode/skills/system-spec-kit/mcp_server/README.md:282:Every search goes through four stages. Each stage has one clear job and cannot change results from earlier stages.
.opencode/skills/system-spec-kit/mcp_server/README.md:284:**Stage 1 -- Gather candidates** using graph-first routing: structural queries dispatch to Code Graph first, then CocoIndex for semantic code discovery, then the spec-doc record pipeline's active channels in parallel. Constitutional-tier memories are always injected regardless of score.
.opencode/skills/system-spec-kit/mcp_server/README.md:309:Before any search runs, the system figures out what kind of help you need. Think of it like a triage nurse who reads your symptoms and routes you to the right specialist.
.opencode/skills/system-spec-kit/mcp_server/README.md:317:| Complex | All 5 | 2,000 tokens | Research, architecture decisions |
.opencode/skills/system-spec-kit/mcp_server/README.md:321:**Query decomposition** splits multi-topic questions into focused sub-queries. Each searches separately and results merge. No LLM call needed.
.opencode/skills/system-spec-kit/mcp_server/README.md:325:**Index-time query surrogates** pre-generate alternative names, summaries and likely questions about content when a spec-doc record is first saved. These are stored alongside the original so future searches match against them too. Like a library cataloger adding subject headings and cross-references to a new book.
.opencode/skills/system-spec-kit/mcp_server/README.md:329:For low-confidence deep searches, the system has two additional fallback strategies:
.opencode/skills/system-spec-kit/mcp_server/README.md:332:- **HyDE (Hypothetical Document Embeddings)** -- writes a hypothetical answer to your question, then searches for real documents matching that imaginary answer. Surfaces content your original wording missed
.opencode/skills/system-spec-kit/mcp_server/README.md:347:| **Research** | Never | 2x slower | 1.5x | 1x | 0.5x | 0.25x |
.opencode/skills/system-spec-kit/mcp_server/README.md:366:When you search, HOT memories get full content in results. WARM memories appear as summaries. COLD and below only show up if they score well enough to earn a spot.
.opencode/skills/system-spec-kit/mcp_server/README.md:405:**Causal trust display badges** -- `memory_search` results carry an additive `trustBadges` payload per `MemoryResultEnvelope`, derived at response time from existing causal-edge columns. The `formatSearchResults()` formatter at `mcp_server/formatters/search-results.ts` batch-reads connected causal-edge data and attaches the following display-only fields to each result envelope: `confidence` (clamped from the strongest connected edge `strength`), `extractionAge` (human-readable age from the newest connected `extracted_at`), `lastAccessAge` (human-readable age from the newest connected `last_accessed`), `orphan` (`true` when the result has no incoming causal edges), and `weightHistoryChanged` (`true` when any connected edge has a `weight_history` row). The formatter fails open when the DB handle or `weight_history` table is unavailable, and preserves any precomputed `trustBadges` payload a caller already supplied. `mcp_server/lib/response/profile-formatters.ts` extends response-profile result typing so the `quick`, `research`, and `resume` profiles preserve the badge payload on `results[]` and `topResult` rather than dropping it during shaping. The placement decision is per-result, not top-level — the trust signal belongs beside the specific spec-doc record claim the user is judging. No schema change, no new relation types, no new storage of code/process/tool facts.
.opencode/skills/system-spec-kit/mcp_server/README.md:448:**Session deduplication** -- pushes down results you already saw. If you got a result 3 turns ago, new searches rank it lower. Saves approximately 50% of tokens on follow-up queries.
.opencode/skills/system-spec-kit/mcp_server/README.md:464:The system also learns from how you use search results:
.opencode/skills/system-spec-kit/mcp_server/README.md:472:**Mode-aware response profiles** -- formats results differently by situation. Quick lookup returns top answer only. Research returns full results with evidence. Resume returns state plus next-steps. Debug returns the full retrieval trace.
.opencode/skills/system-spec-kit/mcp_server/README.md:474:**Empty result recovery** -- diagnoses why a search came back empty (too narrow filter, unclear question, missing knowledge) and suggests next steps.
.opencode/skills/system-spec-kit/mcp_server/README.md:480:Beyond the core search pipeline, several enhancements make retrieval smarter at finding what you actually need.
.opencode/skills/system-spec-kit/mcp_server/README.md:484:**Spec folder hierarchy search** -- uses your project folder organization as a retrieval signal. If you are looking at a child folder, the system also checks parent and sibling folders for related information.
.opencode/skills/system-spec-kit/mcp_server/README.md:490:**Memory summary search channel** -- creates a short summary of each spec-doc record when saved and searches against those summaries. Like reading the back-cover blurb of a book.
.opencode/skills/system-spec-kit/mcp_server/README.md:494:**ANCHOR-based section retrieval** -- indexed packet docs and generated continuity artifacts can include `<!-- ANCHOR:name -->` markers. The search system indexes individual sections separately, allowing retrieval of just "decisions" or "next-steps" from a large document (~93% token savings). Files above 50K characters are always chunk-split.
.opencode/skills/system-spec-kit/mcp_server/README.md:508:**Embedding retry orchestrator** -- when the embedding service is temporarily unavailable, the spec-doc record is saved without a vector and queued for retry. A background worker retries until it succeeds. A temporary outage never permanently blocks full searchability.
.opencode/skills/system-spec-kit/mcp_server/README.md:510:**Lexical-only fallback indexing** -- saves memories in a simpler text-searchable form when the embedding service is down. Keyword search still works. When the service returns, the system upgrades to full vector searchability automatically.
.opencode/skills/system-spec-kit/mcp_server/README.md:514:**Chunked-save finalization** -- chunked saves track the created parent and child IDs so finalization stays transactional. Prediction-error supersede finalization records cross-path `supersedes` edges and marks predecessors superseded inside one transaction. Safe-swap updates null old-child `parent_id` values before bulk delete inside that same finalization step, and any finalize failure triggers compensating cleanup that removes the staged replacement chunk tree. Parent BM25 mutation is delayed until at least one chunk succeeds and, for safe-swap updates, until finalization completes, which preserves the old parent BM25 state when all chunks fail.
.opencode/skills/system-spec-kit/mcp_server/README.md:516:**Dynamic server instructions** -- at startup, tells the calling AI how many memories are stored, how many folders exist and which search methods are available.
.opencode/skills/system-spec-kit/mcp_server/README.md:522:Research-grade infrastructure for measuring and improving search quality over time.
.opencode/skills/system-spec-kit/mcp_server/README.md:524:**12-metric core computation** -- grades every query across twelve quality dimensions (MRR@1/3/10, NDCG@10, MAP and more). Together they pinpoint exactly where search is struggling, like a doctor running multiple tests instead of just asking "do you feel sick?"
.opencode/skills/system-spec-kit/mcp_server/README.md:528:**Ablation study framework** -- turns off each search channel one at a time and measures quality degradation (Recall@20 delta). Identifies which components are critical.
.opencode/skills/system-spec-kit/mcp_server/README.md:542:**Architecture:** CocoIndex (semantic, external MCP) finds code by concept. Code Graph (structural, this server) maps imports, calls and hierarchy. Memory (session, this server) preserves decisions. The compact-merger combines all three under a 4000-token budget for compaction injection. Code-graph source is self-contained under `code-graph/` with `handlers/`, `lib/`, `tools/`, and `tests/`.
.opencode/skills/system-spec-kit/mcp_server/README.md:552:**Edge explanation and blast-radius uplift:** Edge metadata writes include graph-local `reason` and `step` JSON fields next to the existing `confidence`, `detectorProvenance`, and `evidenceClass` payload. `code_graph_query` relationship rows surface those fields for each edge, and `code_graph_context` propagates them through both structured edges and compact text briefs. `blast_radius` keeps the prior file-oriented payload while adding `depthGroups`, `riskLevel` (graph-local: `high` on ambiguity or depth-one fanout >10, `medium` on 4-10, `low` otherwise), an optional `minConfidence` traversal filter, `ambiguityCandidates`, and a structured `failureFallback` so callers never receive a bare error string when resolution cannot continue. The `code_edges` schema stays at `metadata TEXT` — the new fields ride inside the existing JSON blob.
.opencode/skills/system-spec-kit/mcp_server/README.md:556:**Read-path readiness:** `ensureCodeGraphReady()` runs automatically inside `code_graph_query` and `code_graph_context`. It checks graph freshness, returns a `readiness` block, and performs bounded inline selective reindex only when the stale set is small enough to repair safely on the read path. Empty graphs, large stale sets, and other full-scan cases remain explicit `code_graph_scan` work.
.opencode/skills/system-spec-kit/mcp_server/README.md:564:**CALLS disambiguation:** `code_graph_query` CALLS mode prefers callable implementation nodes over wrapper-shadow candidates for ambiguous subjects (e.g. `handle*`), and records ambiguity / selected-candidate metadata alongside the results so callers can audit the choice.
.opencode/skills/system-spec-kit/mcp_server/README.md:566:**Query routing:** Structural queries (callers, imports, dependencies) go to `code_graph_query`. Semantic and concept queries go to CocoIndex (`mcp__cocoindex_code__search`). Session and memory queries go to `memory_context`.
.opencode/skills/system-spec-kit/mcp_server/README.md:612:**Start here for most tasks**: `memory_context` (L1) automatically figures out what you need. Use the lower-level tools when you want precise control.
.opencode/skills/system-spec-kit/mcp_server/README.md:618:##### `memory_context`
.opencode/skills/system-spec-kit/mcp_server/README.md:620:The smart entry point. You describe what you need and it figures out the best way to find it. It reads your query, detects whether you are looking for a decision, debugging context or general knowledge, picks the right search mode and returns the most relevant results. Start here for almost everything.
.opencode/skills/system-spec-kit/mcp_server/README.md:641:  "tool": "memory_context",
.opencode/skills/system-spec-kit/mcp_server/README.md:655:Resume session with combined memory, code graph and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. The response carries freshness-aware code-graph status (`fresh`, `stale`, `empty`, `error`) instead of count-only health. Session-resume auth binds `args.sessionId` to the transport caller context from `lib/context/caller-context.ts`; mismatches are rejected by default, with `MCP_SESSION_RESUME_AUTH_MODE=permissive` available for canary rollout. For the canonical first-call recovery path on session start or after `/clear`, prefer `session_bootstrap`, and for operator-facing packet recovery prefer `/spec_kit:resume`, which reconstructs context from `handover.md`, then `_memory.continuity`, then packet docs.
.opencode/skills/system-spec-kit/mcp_server/README.md:660:| `minimal` | boolean | Skip heavy memory context, return code graph, CocoIndex, structural context, hints, and optional session quality without the full memory payload |
.opencode/skills/system-spec-kit/mcp_server/README.md:676:##### `memory_search`
.opencode/skills/system-spec-kit/mcp_server/README.md:678:The main search tool. You type what you are looking for in plain language and the system searches through all stored knowledge to find the best matches. It understands meaning (beyond keywords), so searching for "login problems" can find a document titled "authentication troubleshooting."
.opencode/skills/system-spec-kit/mcp_server/README.md:682:| `query` | string | Free-text search (use `query` OR `concepts`, not both) |
.opencode/skills/system-spec-kit/mcp_server/README.md:683:| `concepts` | string[] | AND search: 2-5 strings that must all match |
.opencode/skills/system-spec-kit/mcp_server/README.md:699:  "tool": "memory_search",
.opencode/skills/system-spec-kit/mcp_server/README.md:711:##### `memory_quick_search`
.opencode/skills/system-spec-kit/mcp_server/README.md:713:The lightweight search option. Works like a preset: you provide a query and optional scope boundaries and it forwards to the full search tool with sensible defaults. Use this when you want fast results without setting lots of parameters.
.opencode/skills/system-spec-kit/mcp_server/README.md:717:| `query` | string | **Required.** Free-text search query |
.opencode/skills/system-spec-kit/mcp_server/README.md:726:##### `memory_match_triggers`
.opencode/skills/system-spec-kit/mcp_server/README.md:728:The speed-first search option. Instead of doing a deep analysis of your question, it matches specific phrases against a list of known keywords, like a phone's autocomplete. Results come back almost instantly. Frequently used memories show up with full details. Older ones appear as lightweight pointers.
.opencode/skills/system-spec-kit/mcp_server/README.md:740:  "tool": "memory_match_triggers",
.opencode/skills/system-spec-kit/mcp_server/README.md:753:This is how you add new knowledge to the system. Point it at a markdown file and it reads, validates, embeds and stores the content so it becomes searchable. Before storing, it checks whether the information already exists and decides whether to add it fresh, update an older version or skip it. Quality gates catch low-value content before it clutters the knowledge base.
.opencode/skills/system-spec-kit/mcp_server/README.md:816:Run a health check. This is the diagnostic tool for when search quality degrades or something feels off. It checks for stale indexes, divergent aliases, broken embeddings and other issues. It can also attempt automatic repairs.
.opencode/skills/system-spec-kit/mcp_server/README.md:854:Change a spec-doc record's title, keywords or importance without deleting and re-creating it. When you change the title, the search index updates automatically. If the update fails partway through, everything rolls back to the way it was before.
.opencode/skills/system-spec-kit/mcp_server/README.md:869:Tell the system whether a search result was helpful. Helpful results get a confidence boost so they show up more often. Unhelpful results get demoted. Over time, the system learns which memories are genuinely useful, like training a recommendation engine with thumbs-up and thumbs-down.
.opencode/skills/system-spec-kit/mcp_server/README.md:1028:Run a controlled experiment to test which search channels contribute most to finding the right results. Like a scientist removing one ingredient at a time to see which ones matter. Requires `SPECKIT_ABLATION=true` environment variable.
.opencode/skills/system-spec-kit/mcp_server/README.md:1044:Generate a report showing search performance trends over time. Aggregates metrics by sprint and channel.
.opencode/skills/system-spec-kit/mcp_server/README.md:1056:##### `code_graph_query`
.opencode/skills/system-spec-kit/mcp_server/README.md:1060:When readiness requires a full scan that cannot run inline, `code_graph_query` returns the same explicit `status: "blocked"` payload as `code_graph_context` (with `data.blocked`, `graphAnswersOmitted`, `requiredAction: "code_graph_scan"`, `blockReason: "full_scan_required"`, readiness, and `lastPersistedAt`) instead of empty results. CALLS mode on ambiguous subjects (e.g. `handle*`) prefers callable implementation nodes over wrapper-shadow candidates and returns ambiguity / selected-candidate metadata so callers can audit the choice.
.opencode/skills/system-spec-kit/mcp_server/README.md:1073:##### `code_graph_context`
.opencode/skills/system-spec-kit/mcp_server/README.md:1075:Get LLM-oriented compact graph neighborhoods. Accepts CocoIndex search results as seeds for structural expansion. Modes: `neighborhood` (1-hop calls plus imports), `outline` (file symbols), `impact` (reverse callers). Successful responses return `status: "ok"` plus readiness/trust metadata, resolved anchors, graph context, and `data.metadata.partialOutput` so callers can see whether deadline or token-budget pressure produced partial output. When the read path determines the graph needs a full scan, the tool returns an explicit `status: "blocked"` payload with `data.blocked`, `graphAnswersOmitted`, `requiredAction: "code_graph_scan"`, and the same readiness/trust metadata instead of partial graph answers.
.opencode/skills/system-spec-kit/mcp_server/README.md:1082:| `seeds` | array | Seeds from CocoIndex, manual input or graph lookups |
.opencode/skills/system-spec-kit/mcp_server/README.md:1084:| `profile` | string | Output density: `quick`, `research` or `debug` |
.opencode/skills/system-spec-kit/mcp_server/README.md:1177:Read-only preflight MCP tool backed by the handler at `code_graph/handlers/detect-changes.ts`. Maps a unified-diff input to the structural symbols it touches via line-range overlap, refusing to answer when the graph is stale. Registered in `code_graph/handlers/index.ts`, the dispatcher `code_graph/tools/code-graph-tools.ts`, the JSON schema catalog `tool-schemas.ts`, and the strict Zod validator in `schemas/tool-input-schemas.ts`. External clients call it as a top-level MCP tool alongside `code_graph_query` and `code_graph_context`.
.opencode/skills/system-spec-kit/mcp_server/README.md:1190:Check CocoIndex availability, binary path and index status.
.opencode/skills/system-spec-kit/mcp_server/README.md:1194:| _(none required)_ |  | Returns CocoIndex health |
.opencode/skills/system-spec-kit/mcp_server/README.md:1200:Trigger CocoIndex incremental or full re-indexing of the workspace.
.opencode/skills/system-spec-kit/mcp_server/README.md:1210:Submit quality feedback on CocoIndex search results to improve future searches.
.opencode/skills/system-spec-kit/mcp_server/README.md:1214:| `query` | string | **Required.** The search query that was executed |
.opencode/skills/system-spec-kit/mcp_server/README.md:1233:├── api/                       # Stable public imports for eval, indexing, search, providers, storage
.opencode/skills/system-spec-kit/mcp_server/README.md:1235:├── configs/                   # Cognitive config + search-weights reference data
.opencode/skills/system-spec-kit/mcp_server/README.md:1259:| `handlers/chunking-orchestrator.ts` | Handles chunked-save staging, safe-swap finalization, rollback cleanup, and delayed parent BM25 updates. |
.opencode/skills/system-spec-kit/mcp_server/README.md:1260:| `api/index.ts` | Stable external import surface for eval, indexing, search, provider, and discovery helpers. |
.opencode/skills/system-spec-kit/mcp_server/README.md:1281:| L2 | Core | 4 | 1,500 | The main search and save operations |
.opencode/skills/system-spec-kit/mcp_server/README.md:1287:| L8 | Code Graph + Skill Graph + CocoIndex bridge + Skill Advisor | 15 | 1,400 | Code graph scan/query/status/context, `detect_changes`, skill graph + advisor (`advisor_recommend`/`advisor_status`/`advisor_validate`), CocoIndex bridge (`ccc_status`/`ccc_reindex`/`ccc_feedback`) |
.opencode/skills/system-spec-kit/mcp_server/README.md:1306:The system needs an embedding provider to convert text into vectors for similarity search. Pick one:
.opencode/skills/system-spec-kit/mcp_server/README.md:1352:  "tool": "memory_context",
.opencode/skills/system-spec-kit/mcp_server/README.md:1422:    "specFolder": "specs/022-hybrid-rag-fusion"
.opencode/skills/system-spec-kit/mcp_server/README.md:1435:    "specFolder": "specs/022-hybrid-rag-fusion",
.opencode/skills/system-spec-kit/mcp_server/README.md:1465:    "specFolder": "specs/022-hybrid-rag-fusion"
.opencode/skills/system-spec-kit/mcp_server/README.md:1489:    "specFolder": "specs/022-hybrid-rag-fusion",
.opencode/skills/system-spec-kit/mcp_server/README.md:1505:    "specFolder": "specs/022-hybrid-rag-fusion",
.opencode/skills/system-spec-kit/mcp_server/README.md:1526:| Find a past decision | `memory_context` | Set `intent: "find_decision"` |
.opencode/skills/system-spec-kit/mcp_server/README.md:1527:| Search for specific terms | `memory_search` | Use `concepts: ["term1", "term2"]` for AND search |
.opencode/skills/system-spec-kit/mcp_server/README.md:1528:| Check triggers on every prompt | `memory_match_triggers` | Pass the user's prompt text |
.opencode/skills/system-spec-kit/mcp_server/README.md:1530:| Diagnose search problems | `memory_health` | Set `reportMode: "full"` |
.opencode/skills/system-spec-kit/mcp_server/README.md:1544:**What you see**: Irrelevant or low-scoring results from `memory_search` or `memory_context`.
.opencode/skills/system-spec-kit/mcp_server/README.md:1546:**Common causes**: Stale BM25 index, divergent aliases in FTS5 or memories with low quality scores surfacing.
.opencode/skills/system-spec-kit/mcp_server/README.md:1555:{ "tool": "memory_search", "arguments": { "query": "your query", "min_quality_score": 0.5 } }
.opencode/skills/system-spec-kit/mcp_server/README.md:1578:**What you see**: Saved memories have zero vector scores. Semantic search returns nothing.
.opencode/skills/system-spec-kit/mcp_server/README.md:1631:| BM25 index stale | Set `ENABLE_BM25=false` to fall back to FTS5 |
.opencode/skills/system-spec-kit/mcp_server/README.md:1674:Three main differences. First, this system uses 5 search channels combined with rank fusion, beyond vector similarity. Second, it applies FSRS decay so recently accessed memories rank higher without manual curation. Third, the causal graph lets you answer "why was this decision made?" which no vector database supports natively.
.opencode/skills/system-spec-kit/mcp_server/README.md:1680:Constitutional memories are rules that never change: coding standards, architectural constraints, project non-negotiables. They get the highest importance weight and appear in every search result regardless of score. Store things like "always use TypeScript strict mode" or "never commit secrets" at this tier.
.opencode/skills/system-spec-kit/mcp_server/README.md:1698:Start with `memory_context` for all retrieval tasks. It handles intent detection and routing automatically. Use `memory_search` when you want explicit control over channels. Use `memory_match_triggers` when processing a raw prompt at the start of each turn. Use L4-L7 tools only for mutation, analysis or maintenance.
.opencode/skills/system-spec-kit/mcp_server/README.md:1724:| [lib/search/README.md](./lib/search/README.md) | Per-stage module mapping for the 4-stage search pipeline |
.opencode/skills/system-spec-kit/mcp_server/plugin_bridges/spec-kit-compact-code-graph-bridge.mjs:6:import * as vectorIndex from '../dist/lib/search/vector-index.js';
.opencode/skills/mcp-coco-index/scripts/ensure_ready.sh:12:#   20 - Repo-local CocoIndex binary missing after bootstrap
.opencode/skills/mcp-coco-index/scripts/ensure_ready.sh:170:printf '%s\n' "=== CocoIndex Ensure Ready ==="
.opencode/skills/system-spec-kit/mcp_server/utils/db-helpers.ts:11:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/scripts/README.md:79:- Module initialization order: `vectorIndex` -> `embeddings` -> `checkpointsLib` -> `accessTracker` -> `hybridSearch` -> `initDbState` -> `setEmbeddingModelReady`.
.opencode/skills/mcp-coco-index/tests/test_e2e.py:6:"""End-to-end tests exercising the full CLI → daemon → index → search flow.
.opencode/skills/mcp-coco-index/tests/test_e2e.py:142:    """Init → init (idempotent) → index → status → search variants → daemon status."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:166:    result = runner.invoke(app, ["search", "fibonacci", "calculation"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:171:    result = runner.invoke(app, ["search", "database", "connection"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:176:    result = runner.invoke(app, ["search", "function", "--lang", "python"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:181:    result = runner.invoke(app, ["search", "function", "--path", "lib/*"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:187:        app, ["search", "xyzzy_nonexistent_symbol_12345"], catch_exceptions=False
.opencode/skills/mcp-coco-index/tests/test_e2e.py:198:    """Init → index → add new file → re-index → search finds new content."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:211:    result = runner.invoke(app, ["search", "handleRequest"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:217:    """Init → index → search → reset (dbs only) → re-index → search works again."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:222:    result = runner.invoke(app, ["search", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:249:    result = runner.invoke(app, ["search", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:255:    """Init → index → reset --all → verify full cleanup → search errors."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:276:    result = runner.invoke(app, ["search", "fibonacci"])
.opencode/skills/mcp-coco-index/tests/test_e2e.py:282:    """Init → index → reset --all → re-init → re-index → search works again."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:302:    result = runner.invoke(app, ["search", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:339:    """Init → index → daemon stop → index auto-starts daemon → search works."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:352:    result = runner.invoke(app, ["search", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:359:    """Init → index → daemon restart → re-index → search works."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:373:    result = runner.invoke(app, ["search", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:379:def test_session_search_refresh() -> None:
.opencode/skills/mcp-coco-index/tests/test_e2e.py:380:    """Init (no explicit index) → search --refresh indexes then searches."""
.opencode/skills/mcp-coco-index/tests/test_e2e.py:383:    # search --refresh without prior explicit index
.opencode/skills/mcp-coco-index/tests/test_e2e.py:384:    result = runner.invoke(app, ["search", "--refresh", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:403:    result = runner.invoke(app, ["search", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:409:    result = runner.invoke(app, ["search", "database", "connection"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:413:    # From lib/, searching for fibonacci should NOT find main.py (outside lib/)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:414:    result = runner.invoke(app, ["search", "fibonacci"], catch_exceptions=False)
.opencode/skills/mcp-coco-index/tests/test_e2e.py:427:    result = runner.invoke(app, ["search", "hello"])
.opencode/skills/mcp-coco-index/scripts/common.sh:5:# Shared helpers for CocoIndex skill scripts.
.opencode/skills/mcp-coco-index/scripts/common.sh:203:        printf '%s\n' "Restore the local mcp-coco-index skill payload before using CocoIndex automation."
.opencode/skills/mcp-coco-index/scripts/common.sh:207:        printf '%s\n' "Restore the CocoIndex helper scripts under .opencode/skills/mcp-coco-index/scripts."
.opencode/skills/mcp-coco-index/scripts/common.sh:223:        printf '%s\n' "Restart the CocoIndex daemon or run a warm-up search before requiring daemon readiness."
.opencode/skills/mcp-coco-index/scripts/common.sh:227:        printf '%s\n' "Daemon will auto-start on the next ccc search or ccc index command."
.opencode/skills/mcp-coco-index/scripts/common.sh:230:    printf '%s\n' "Semantic search is ready. Use MCP search first, then follow-up queries with refresh_index=false."
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:102:  'research_finding',
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:142:const coverageGraphLoopTypeEnum = z.enum(['research', 'review']);
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:171:  includeTrace: z.boolean().optional(), // CHK-040: Forward to internal memory_search
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:174:  profile: z.enum(['quick', 'research', 'resume', 'debug']).optional(),
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:210:  profile: z.enum(['quick', 'research', 'resume', 'debug']).optional(),
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:213:// E3: Simplified search schema — 3 params only
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:282:  searchMode: z.string().optional(),
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:490:  profile: z.enum(['quick', 'research', 'debug']).optional(),
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:586:  memory_context: memoryContextSchema as unknown as ToolInputSchema,
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:587:  memory_search: memorySearchSchema as unknown as ToolInputSchema,
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:588:  memory_quick_search: memoryQuickSearchSchema as unknown as ToolInputSchema,
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:589:  memory_match_triggers: memoryMatchTriggersSchema as unknown as ToolInputSchema,
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:616:  code_graph_query: codeGraphQuerySchema as unknown as ToolInputSchema,
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:618:  code_graph_context: codeGraphContextSchema as unknown as ToolInputSchema,
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:646:  memory_context: ['input', 'mode', 'intent', 'specFolder', 'tenantId', 'userId', 'agentId', 'limit', 'sessionId', 'enableDedup', 'includeContent', 'includeTrace', 'tokenUsage', 'anchors', 'profile'],
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:647:  memory_search: ['cursor', 'query', 'concepts', 'specFolder', 'tenantId', 'userId', 'agentId', 'limit', 'sessionId', 'enableDedup', 'tier', 'contextType', 'useDecay', 'includeContiguity', 'includeConstitutional', 'enableSessionBoost', 'enableCausalBoost', 'includeContent', 'anchors', 'min_quality_score', 'minQualityScore', 'bypassCache', 'rerank', 'applyLengthPenalty', 'applyStateLimits', 'minState', 'intent', 'autoDetectIntent', 'trackAccess', 'includeArchived', 'mode', 'includeTrace', 'profile'],
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:648:  memory_quick_search: ['query', 'limit', 'specFolder', 'tenantId', 'userId', 'agentId'],
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:649:  memory_match_triggers: ['prompt', 'specFolder', 'tenantId', 'userId', 'agentId', 'limit', 'session_id', 'turnNumber', 'include_cognitive'],
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:656:  memory_validate: ['id', 'wasUseful', 'queryId', 'queryTerms', 'resultRank', 'totalResultsShown', 'searchMode', 'intent', 'sessionId', 'notes'],
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:676:  code_graph_query: ['operation', 'subject', 'subjects', 'unionMode', 'edgeType', 'limit', 'includeTransitive', 'maxDepth', 'minConfidence'],
.opencode/skills/system-spec-kit/mcp_server/schemas/tool-input-schemas.ts:678:  code_graph_context: ['input', 'queryMode', 'subject', 'seeds', 'budgetTokens', 'profile', 'includeTrace'],
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-bulk-delete.ts:8:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/query.py:1:"""Query implementation for codebase search."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/query.py:200:        elif path_class == "spec_research":
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/query.py:202:            ranking_signals.append("spec_research_penalty")
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/query.py:263:    Perform vector similarity search using vec0 KNN index.
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/query.py:265:    Uses sqlite-vec's vec0 virtual table for indexed nearest-neighbor search.
.opencode/skills/system-spec-kit/mcp_server/utils/validators.ts:51:/** Maximum query length for search operations (BUG-007) */
.opencode/skills/system-spec-kit/mcp_server/utils/validators.ts:59: * Validate and normalize a search query
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:2:title: "CocoIndex Code Installation Guide"
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:3:description: "Complete installation and configuration guide for the CocoIndex Code MCP server providing semantic code search via vector embeddings."
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:10:# CocoIndex Code Installation Guide
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:12:Complete installation and configuration guide for CocoIndex Code, a semantic code search engine for AI-assisted development. Provides natural language code search across your entire codebase with configurable embedding models (local or API-based). Runs as an MCP server exposing a single `search` tool to AI assistants, while `status`, `index`, `reset`, and `daemon` remain CLI commands.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:27:I want to install CocoIndex Code for semantic code search.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:34:5. Verify with a test search: ccc search "error handling"
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:46:- Test with a sample semantic search query
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:56:3. Run: `.opencode/skills/mcp-coco-index/mcp_server/.venv/bin/ccc search "hello world"`
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:87:CocoIndex Code gives AI assistants the ability to search your codebase by meaning rather than exact text. Ask "how does authentication work" and it finds relevant code across files and languages, even when the word "authentication" never appears in the source.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:107:| Find code by meaning or intent            | CocoIndex Code | Understands concepts, not just keywords           |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:110:| Understand how a feature is implemented    | CocoIndex Code | Finds related code across files                   |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:113:Default to Grep for exact matches. Use CocoIndex Code when you need semantic understanding.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:143:|              CocoIndex Code MCP Server                       |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:146:|  MCP Tool: search only                                      |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:162:| Semantic search   | <2s    | ~500ms    |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:310:Connect CocoIndex Code to your AI assistant (Phase 4). The MCP server runs via `ccc mcp` in stdio mode.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:313:- `COCOINDEX_CODE_ROOT_PATH` - The root directory of the project to search. Set this to your project root.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:435:CocoIndex Code supports multiple embedding models. Configure via `~/.cocoindex_code/global_settings.yml`.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:437:**Primary (recommended):** `voyage/voyage-code-3` via LiteLLM provider -- best code search quality. Requires `VOYAGE_API_KEY`.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:440:# Voyage Code 3 (recommended - best code search quality)
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:494:  $CCC search "hello" --limit 3 2>&1 && \
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:507:| 5   | Search works   | `ccc search "test"`         | Results returned            |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:517:Expected result: The AI uses the CocoIndex Code search tool and returns relevant code snippets with file paths and relevance scores.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:521:All 6 checklist items above pass with no errors. Your AI client successfully runs a semantic search on request.
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:535:ccc search "authentication middleware"
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:542:ccc search "database connection" --lang python
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:543:# Only searches Python files
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:549:ccc search "error handling" --path src/api/
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:550:# Only searches within the src/api/ directory
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:556:ccc search "configuration" --limit 5 --offset 10
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:566:# Force refresh during search
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:567:ccc search "my query" --refresh
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:581:| "How does X work?"                     | CocoIndex Code | Semantic understanding         |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:584:| Understand feature implementation      | CocoIndex Code | Cross-file concept search      |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:586:| "Where is error handling done?"        | CocoIndex Code | Intent-based search            |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:620:| **Recommended** | Voyage Code 3 via LiteLLM (API key required, best code search quality)      |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:628:| `ccc search`      | Semantic search across codebase      |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:640:| `search`   | query (required), lang, path, limit, offset         | Semantic code search       |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:655:ccc search "how does user authentication work"
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:662:ccc search "database migration" --lang python
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:669:ccc search "API route handlers" --path src/routes/ --limit 5
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:676:ccc search "error handling and recovery" --lang typescript
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:683:ccc search "unit test setup and teardown"
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:796:| Search Patterns     | `.opencode/skills/mcp-coco-index/references/search_patterns.md`      | Query strategies       |
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:841:ccc search "query"                        # Basic search
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:842:ccc search "query" --lang python          # Language filter
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:843:ccc search "query" --path src/            # Path filter
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:844:ccc search "query" --limit 5             # Limit results
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:845:ccc search "query" --offset 10           # Pagination
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:846:ccc search "query" --refresh             # Force index refresh
.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md:866:| `phase_5_complete`  | End-to-end search operational        |
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/prompt-policy.ts:92:  'deep research',
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:7:type Shape = 'review' | 'research';
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:89:  it('renders a research-shaped resource map with per-iteration citation counts', () => {
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:91:      shape: 'research',
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:93:      scope: 'research convergence output for packet 003',
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:103:              '.opencode/commands/spec_kit/deep-research.md',
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:104:              '.opencode/skills/sk-deep-research/references/convergence.md',
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:107:              { path: '.opencode/skills/sk-deep-research/SKILL.md' },
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:108:              { path: '.opencode/specs/system-spec-kit/demo/research.md' },
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:114:            source_paths: ['.opencode/commands/spec_kit/deep-research.md'],
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:116:              { path: '.opencode/skills/sk-deep-research/SKILL.md' },
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:123:            source_paths: ['.opencode/commands/spec_kit/deep-research.md'],
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:125:              { path: '.opencode/skills/sk-deep-research/SKILL.md' },
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:126:              { path: 'notes/research-support.txt' },
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:146:      '| .opencode/commands/spec_kit/deep-research.md | Cited | OK | Citations=3; Iterations=3 |',
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:149:      '| .opencode/skills/sk-deep-research/SKILL.md | Cited | OK | Citations=3; Iterations=3 |',
.opencode/skills/system-spec-kit/mcp_server/scripts/tests/resource-map-extractor.vitest.ts:152:      '| .opencode/specs/system-spec-kit/demo/research.md | Cited | MISSING | Citations=1; Iterations=1 |',
.opencode/skills/mcp-coco-index/tests/test_daemon.py:195:def test_daemon_search_after_index(daemon_sock: str, daemon_project: str) -> None:
.opencode/skills/mcp-coco-index/tests/test_daemon.py:246:def test_daemon_search_waits_during_explicit_index(daemon_sock: str) -> None:
.opencode/skills/mcp-coco-index/tests/test_daemon.py:248:    IndexWaitingNotice (Path B: index first, then search)."""
.opencode/skills/mcp-coco-index/tests/test_daemon.py:249:    # Use enough files to ensure indexing takes long enough for the search to
.opencode/skills/mcp-coco-index/tests/test_daemon.py:251:    project = Path(tempfile.mkdtemp(prefix="ccc_idx_then_search_"))
.opencode/skills/mcp-coco-index/tests/test_daemon.py:264:    # Send the search request immediately — the daemon processes requests
.opencode/skills/mcp-coco-index/tests/test_daemon.py:281:        raise AssertionError(f"Unexpected response on search conn: {type(resp).__name__}")
.opencode/skills/mcp-coco-index/tests/test_daemon.py:293:def test_daemon_search_waits_for_load_time_indexing(daemon_sock: str) -> None:
.opencode/skills/mcp-coco-index/tests/test_daemon.py:326:    # Second search — load-time indexing is done, no waiting expected
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/config.py:137:        """Path to the CocoIndex state database."""
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/LICENSE:189:   Copyright 2026 CocoIndex Inc
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:7:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:8:// Feature catalog: BM25 trigger phrase re-index gate
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:42:import { initialize_db } from '../lib/search/vector-index-store.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:149:    console.warn('[memory_match_triggers] Failed to fetch memory records:', message);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:183:/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:196:      tool: 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:217:      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:219:        tool: 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:224:          hint: 'Omit session_id to start a new server-generated session, or reuse the effectiveSessionId returned by memory_context.',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:283:      console.warn('[memory_match_triggers] Decay failed:', message);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:322:      console.error('[memory_match_triggers] Scope filtering failed, returning empty results (fail-closed):', toErrorMessage(scopeErr));
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:333:      tool: 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:371:        console.warn(`[memory_match_triggers] Failed to activate memory ${match.memoryId}:`, message);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:387:          console.warn(`[memory_match_triggers] Co-activation failed for ${memoryId}:`, message);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:488:    console.warn(`[memory_match_triggers] Latency ${latencyMs}ms exceeds 100ms target`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:508:    tool: 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:559:const handle_memory_match_triggers = handleMemoryMatchTriggers;
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:562:  handle_memory_match_triggers,
.opencode/skills/system-spec-kit/mcp_server/formatters/index.ts:28:} from './search-results.js';
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:906:  // Reserve unsent hashes while filtering so concurrent searches cannot both inject.
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1263:      ? `memory_search({ sessionId: "${sessionId}" })`
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-manager.ts:1264:      : 'memory_search({ query: "last session" })';
.opencode/skills/mcp-coco-index/tests/test_cli_helpers.py:88:    assert "# CocoIndex Code (ccc)" in content
.opencode/skills/mcp-coco-index/tests/test_cli_helpers.py:118:    gitignore.write_text("*.pyc\n# CocoIndex Code (ccc)\n/.cocoindex_code/\n__pycache__/\n")
.opencode/skills/mcp-coco-index/tests/test_cli_helpers.py:122:    assert "# CocoIndex Code (ccc)" not in content
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:2:title: "CocoIndex Code: Manual Testing Playbook"
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:3:description: "Operator-facing reference combining the manual testing directory, integrated review/orchestration guidance, execution expectations, and per-feature validation files for the CocoIndex Code skill."
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:6:# CocoIndex Code: Manual Testing Playbook
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:18:- `02--mcp-search-tool/`
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:36:- [8. MCP SEARCH TOOL](#8--mcp-search-tool)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:63:- CocoIndex daemon is available via `ccc` and `ccc status` responds.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:65:- The MCP search tool is available in the current session.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:84:- MCP calls are shown as `mcp__cocoindex_code__search({ ... })`.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:104:- Wave 4 covers code-graph integration scenarios that need both CocoIndex and Spec Kit Memory surfaces healthy.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:118:Prompt summary: As a manual-testing orchestrator, initialize a new CocoIndex Code project in the current directory against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 2: output contains "Initialized" or creates .cocoindex_code/; Step 3: file exists; Step 4: output contains "already" or exits without error; Step 5: succeeds without error; Step 6: file exists. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:131:Prompt summary: As a manual-testing orchestrator, build the full semantic index for this project against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Output contains numeric file and chunk counts (for example "Files:" and "Chunks:" or similar metric lines). Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:144:Prompt summary: As a manual-testing orchestrator, create a temp file, reindex, search for it, delete it, reindex again against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 3: search returns at least 1 result referencing ccc_test_incremental.py; Step 6: search returns 0 results for that file. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:146:Expected signals: Step 3: search returns at least 1 result referencing `ccc_test_incremental.py`; Step 6: search returns 0 results for that file
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:151:### CCC-004 | CLI search with filters
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:157:Prompt summary: As a manual-testing orchestrator, search for "function" filtered to Python and TypeScript with limit 3 against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: returns results; Step 2: all file extensions are .py, .ts, or .tsx; Step 3: result count <= 3. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:162:> **Feature File:** [CCC-004](01--core-cli-commands/004-cli-search-with-filters.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:170:Prompt summary: As a manual-testing orchestrator, reset the CocoIndex Code index completely and rebuild against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: exits without error; Step 2: shows zero files or "not initialized"; Step 4: rebuilds with non-zero counts; Step 5: shows non-zero file and chunk counts. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:184:### MCP-001 | Basic semantic search
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:187:Verify MCP search returns results with file paths, scores, and line ranges.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:190:Prompt summary: As a manual-testing orchestrator, use CocoIndex to search for "fibonacci calculation" against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results array with at least 1 entry; each entry contains file (string), score (float 0.0-1.0), lines (start/end), snippet (string), language (string). Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:195:> **Feature File:** [MCP-001](02--mcp-search-tool/001-basic-semantic-search.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:203:Prompt summary: As a manual-testing orchestrator, search CocoIndex for "function" filtered to Python only against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify All result file paths end in .py; no .ts, .js, .go, etc. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:208:> **Feature File:** [MCP-002](02--mcp-search-tool/002-language-filter-single.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:216:Prompt summary: As a manual-testing orchestrator, search CocoIndex for "function" in both Python and JavaScript against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results contain mix of .py and .js files; no other extensions. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:221:> **Feature File:** [MCP-003](02--mcp-search-tool/003-language-filter-multi.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:229:Prompt summary: As a manual-testing orchestrator, search CocoIndex for "skill" only under .opencode/skills/ against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify All result paths begin with .opencode/skills/; no results from other directories. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:234:> **Feature File:** [MCP-004](02--mcp-search-tool/004-path-filter.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:242:Prompt summary: As a manual-testing orchestrator, search CocoIndex for "config" in Python under .opencode/ with 2 results against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Result count <= 2; all files are .py; all paths start with .opencode/. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:247:> **Feature File:** [MCP-005](02--mcp-search-tool/005-combined-filters.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:255:Prompt summary: As a manual-testing orchestrator, compare CocoIndex search with 1 result vs 10 results against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 2: exactly 1 result; Step 4: result count between 1 and 10 (inclusive); Step 4 count >= Step 2 count. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:260:> **Feature File:** [MCP-006](02--mcp-search-tool/006-result-limit.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:262:### MCP-007 | No-refresh search
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:268:Prompt summary: As a manual-testing orchestrator, search CocoIndex for "test" without triggering a reindex against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results array is non-empty; response time is noticeably faster than a refreshing search (no index wait notice). Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:270:Expected signals: Results array is non-empty; response time is noticeably faster than a refreshing search (no index wait notice)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:273:> **Feature File:** [MCP-007](02--mcp-search-tool/007-no-refresh-search.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:281:Prompt summary: As a manual-testing orchestrator, fire two MCP CocoIndex searches concurrently with refresh_index=true against the current CocoIndex daemon in this repository. Verify either both responses are valid result arrays OR at least one response surfaces a ComponentContext error string (acceptable failure mode per SKILL.md §4). Confirm that switching the second call to refresh_index=false eliminates the error. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:286:> **Feature File:** [MCP-008](02--mcp-search-tool/008-concurrent-refresh-race.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:301:Prompt summary: As a manual-testing orchestrator, check the CocoIndex Code global settings for the embedding model against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Settings file exists; embedding.model matches a documented model such as the default local sentence-transformers/all-MiniLM-L6-v2 or a LiteLLM model like voyage/voyage-code-3. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:314:Prompt summary: As a manual-testing orchestrator, inspect the CocoIndex Code project settings for language coverage against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify include_patterns. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:327:Prompt summary: As a manual-testing orchestrator, check the CocoIndex Code status for this initialized project against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Output shows numeric file count > 0 and numeric chunk count > 0. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:342:Expected signals: `ccc status` invoked from the subdirectory with the env var set reports the same file/chunk counts as `ccc status` invoked at the env-var-pinned root; `ccc search --limit 1` returns a path under the env-var-pinned root
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:360:Prompt summary: As a manual-testing orchestrator, stop the daemon, then search -- against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify auto-start against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: daemon stops or reports already stopped; Step 3: search returns at least 1 result; Step 5: daemon reports running. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:362:Expected signals: Step 1: daemon stops or reports already stopped; Step 3: search returns at least 1 result; Step 5: daemon reports running
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:373:Prompt summary: As a manual-testing orchestrator, check daemon status and against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify runtime files against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: output includes version or uptime information; Step 2: both daemon.pid and daemon.sock files exist. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:386:Prompt summary: As a manual-testing orchestrator, run doctor.sh --json --strict --require-config followed by ensure_ready.sh --json --strict --require-config against the current CocoIndex install in this repository. Verify both scripts exit 0 with healthy JSON; rerun ensure_ready.sh and confirm idempotency; then run both scripts from a temp directory with no .cocoindex_code/ to confirm --require-config makes them exit non-zero with an explicit reason. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:403:Verify `--semantic` triggers CocoIndex search and `!semantic(...)` appears in reason field when skill references found.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:406:Prompt summary: As a manual-testing orchestrator, test skill advisor with semantic search for a deployment query against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify JSON output is valid; at least one recommendation entry contains !semantic( in its reason field; CocoIndex search was invoked (visible in processing or reason text). Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:408:Expected signals: JSON output is valid; at least one recommendation entry contains `!semantic(` in its `reason` field; CocoIndex search was invoked (visible in processing or reason text)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:419:Prompt summary: As a manual-testing orchestrator, run skill advisor twice for the same deployment query: first without semantic hits, then with pre-computed CocoIndex hits against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify sk-git appears in the semantic-hits run, its confidence is higher than in the baseline run, and the boosted reason references semantic input. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:436:Verify search returns empty results gracefully for a nonsense query (no crash, no error).
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:439:Prompt summary: As a manual-testing orchestrator, search for a completely nonsensical term that has no matches against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Response is valid (not an exception or error); result array is empty or contains zero entries; no stack trace. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:456:Verify that semantic queries (containing keywords like "find examples", "how to", "similar to", "explain") are classified as semantic and do not trigger structural graph augmentation in `memory_context`.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:459:Prompt summary: As a manual-testing orchestrator, send a semantic query like "find examples of error handling patterns in this codebase" to memory_context against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Intent classified as 'semantic', routedBackend is semantic when present, no graphContext block in the response, no structural graph data injected into primary results. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:469:Verify that hybrid queries (mixing structural keywords like "function", "calls" with semantic keywords like "explain", "examples") are classified as hybrid and append `graphContext` metadata to the normal `memory_context` response.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:472:Prompt summary: As a manual-testing orchestrator, send a hybrid query like "find all validation functions and explain their error handling approach" to memory_context against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Intent classified as hybrid, response contains queryIntentRouting, graphContext appears when graph seeds resolve, and the normal semantic response body remains present. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:474:Expected signals: Intent classified as `hybrid`, response contains `queryIntentRouting`, `graphContext` appears when graph seeds resolve, and the normal semantic response body remains present
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:477:> **Feature File:** [INT-002](07--code-graph-integration/002-hybrid-query-merges-results.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:479:### INT-003 | Session recovery surfaces include CocoIndex availability status
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:482:Verify that `session_bootstrap` exposes CocoIndex status through `resume.cocoIndex`, that `session_resume` still exposes the direct `cocoIndex` field, and that both surfaces degrade gracefully when the CocoIndex binary is unavailable. `available` reflects whether the `ccc` binary exists at the expected install path, not whether the daemon is currently running. The `binaryPath` must point to the expected `ccc` binary location.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:485:Prompt summary: As a manual-testing orchestrator, call session_bootstrap and session_resume, then examine the CocoIndex status fields against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify session_bootstrap.resume.cocoIndex.available and session_resume.cocoIndex.available match binary presence on disk; both binaryPath values are non-empty strings; session_bootstrap includes structuralContext; both calls complete without error regardless of binary availability. Return a concise user-facing pass/fail verdict with the main reason.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:501:- `test_e2e.py` and `test_e2e_daemon.py`: full CLI, search, and daemon workflow coverage.
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:512:- CCC-004: [CLI search with filters](01--core-cli-commands/004-cli-search-with-filters.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:517:- MCP-001: [Basic semantic search](02--mcp-search-tool/001-basic-semantic-search.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:518:- MCP-002: [Language filter (single)](02--mcp-search-tool/002-language-filter-single.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:519:- MCP-003: [Language filter (multi)](02--mcp-search-tool/003-language-filter-multi.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:520:- MCP-004: [Path filter](02--mcp-search-tool/004-path-filter.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:521:- MCP-005: [Combined filters](02--mcp-search-tool/005-combined-filters.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:522:- MCP-006: [Result limit](02--mcp-search-tool/006-result-limit.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:523:- MCP-007: [No-refresh search](02--mcp-search-tool/007-no-refresh-search.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:524:- MCP-008: [Concurrent refresh_index race](02--mcp-search-tool/008-concurrent-refresh-race.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:551:- INT-002: [Hybrid intent queries add graph context on top of semantic retrieval](07--code-graph-integration/002-hybrid-query-merges-results.md)
.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md:552:- INT-003: [Session recovery surfaces include CocoIndex availability status](07--code-graph-integration/003-session-resume-includes-cocoindex.md)
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:9:with it through ``DaemonClient``, mirroring how ``ccc index`` / ``ccc search``
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:95:def test_index_and_search_via_client(e2e_daemon: tuple[str, Path]) -> None:
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:96:    """Index a project and search via the client, same as ccc index / ccc search."""
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:109:    search_resp = client.search(str(project_dir), query="fibonacci")
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:110:    assert search_resp.success
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:111:    assert len(search_resp.results) > 0
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:112:    assert "main.py" in search_resp.results[0].file_path
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:123:    c1.search(str(project_dir), query="fibonacci")
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:129:    search_resp = c2.search(str(project_dir), query="fibonacci")
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:130:    assert search_resp.success
.opencode/skills/mcp-coco-index/tests/test_e2e_daemon.py:131:    assert len(search_resp.results) > 0
.opencode/skills/system-spec-kit/mcp_server/formatters/README.md:3:description: "Response formatting for search results, anchor filtering metrics, and safe content shaping."
.opencode/skills/system-spec-kit/mcp_server/formatters/README.md:6:  - "search results"
.opencode/skills/system-spec-kit/mcp_server/formatters/README.md:27:`formatters/` converts internal search results into MCP-ready payloads.
.opencode/skills/system-spec-kit/mcp_server/formatters/README.md:30:- `search-results.ts`: formats results, optional content embedding, anchor extraction, and path checks.
.opencode/skills/system-spec-kit/mcp_server/lib/session/README.md:95:1. User queries memory_search
.opencode/skills/system-spec-kit/mcp_server/lib/session/README.md:141:// After retrieving search results
.opencode/skills/system-spec-kit/mcp_server/lib/session/README.md:216:**Symptom**: Expected memories not returned in search results.
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:5:  - "search weights"
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:32:- `search-weights.json` - scoring weights and document-type multipliers for memory search ranking. Partly active, partly reference. Inline notes are the source of truth for what is currently loaded at runtime.
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:40:Current sections in `search-weights.json`:
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:47:Active search tuning that does **not** live in `search-weights.json`:
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:50:- Stage 3 MMR intent lambdas live in `lib/search/intent-classifier.ts`, where continuity-oriented reranking now uses lambda `0.65`.
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:51:- Stage 3 rerank gating lives in `lib/search/pipeline/stage3-rerank.ts`, where `MIN_RESULTS_FOR_RERANK = 4`.
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:52:- Reranker cache behavior and telemetry live in `lib/search/cross-encoder.ts`; `getRerankerStatus()` exposes `hits`, `misses`, `staleHits`, and `evictions` alongside latency stats.
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:73:- Runtime behavior is source-of-truth in the resolver helpers, not in import-time constants. `search-weights.json` is read live where referenced, and environment-gated behavior should be documented against the resolver function that reads it.
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:82:node -e "JSON.parse(require('fs').readFileSync('.opencode/skills/system-spec-kit/mcp_server/configs/search-weights.json', 'utf8'))"
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:93:- `../lib/search/intent-classifier.ts`
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:94:- `../lib/search/pipeline/stage3-rerank.ts`
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:95:- `../lib/search/cross-encoder.ts`
.opencode/skills/system-spec-kit/mcp_server/configs/README.md:96:- `../handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:12:import { isCocoIndexAvailable } from '../utils/cocoindex-path.js';
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:155:  // CocoIndex availability
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:158:    cocoIndexAvailable = isCocoIndexAvailable();
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:185:    routingParts.push('semantic/concept search → mcp__cocoindex_code__search');
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:188:    routingParts.push('structural queries (callers, deps) → code_graph_query');
.opencode/skills/system-spec-kit/mcp_server/lib/session/session-snapshot.ts:249:    recommendedAction = 'Structural context available. Use code_graph_query for structural lookups.';
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:18:Operators running `ccc` from monorepo subtrees, worktrees, or CI runners rely on `COCOINDEX_CODE_ROOT_PATH` to pin the correct project root regardless of cwd. If the env var silently loses to a marker directory closer to cwd, indexing and search will target the wrong project and search results will be silently misleading. No existing scenario asserts this precedence.
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:29:- Expected execution process: identify the current project root with markers; cd into a subdirectory of the project (or any path containing `.git`); export `COCOINDEX_CODE_ROOT_PATH` pointing at the original project root; run `ccc status` and `ccc search` with `--limit 1`; verify the reported file count and result file paths trace back to the env-pinned root.
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:30:- Expected signals: `ccc status` invoked from the subdirectory with the env var set reports the same file/chunk counts as `ccc status` invoked at the env-var-pinned root; a one-result `ccc search` returns a path under the env-var-pinned root, not under cwd.
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:32:- Pass/fail: PASS if env-var-pinned root wins (counts match the root, search results live under the env-var path); FAIL if cwd-derived root wins (counts match the subdirectory, search results live under cwd-derived discovery).
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:49:6. `bash: cd .opencode && export COCOINDEX_CODE_ROOT_PATH=/Users/.../Public && ccc search "skill" --limit 1` — verify result path is under env-var-pinned root, not under `.opencode/`-relative cwd
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:65:- **Pass**: PINNED counts equal BASELINE AND the search result in step 6 traces to a file under the env-var-pinned root.
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:66:- **Fail**: PINNED counts differ from BASELINE (env var was ignored) OR search result in step 6 traces to a path outside the env-var-pinned root (env var was overridden by marker discovery).
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md:71:2. If step 6 returns a path outside the env-var-pinned root: this is the dangerous failure mode — env var lost to marker discovery; capture the search response and escalate as a SKILL.md §3 contract regression.
.opencode/skills/mcp-coco-index/tests/test_protocol.py:47:def test_encode_decode_search_request_with_defaults() -> None:
.opencode/skills/mcp-coco-index/tests/test_protocol.py:57:def test_encode_decode_search_request_with_all_fields() -> None:
.opencode/skills/mcp-coco-index/tests/test_protocol.py:77:def test_encode_decode_search_response_with_results() -> None:
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:5:import { isCocoIndexAvailable } from '../lib/utils/cocoindex-path.js';
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:6:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:8:import { enrichWithRetrievalDirectives } from '../lib/search/retrieval-directives.js';
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:86:  'memory_context',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:87:  'memory_search',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:88:  'memory_quick_search',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:89:  'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:451:  // F046: CocoIndex availability via shared helper (no process.cwd())
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:452:  const cocoIndexAvailable = isCocoIndexAvailable();
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:460:    recommendedCalls.push('memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })');
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:463:    recommendedCalls.push('memory_match_triggers({ prompt: "<your task>" })');
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:468:    toolRoutingRules.push('semantic/concept queries → mcp__cocoindex_code__search');
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:471:    toolRoutingRules.push('structural queries (callers, deps) → code_graph_query');
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:482:      graphRetrieval: 'For broad topic questions, use memory_search with retrievalLevel: "global" for community-level results. For specific memories, use "local" (default). Use "auto" for automatic fallback.',
.opencode/skills/system-spec-kit/mcp_server/hooks/memory-surface.ts:483:      communitySearch: 'When primary search returns weak results, community search fallback activates automatically (SPECKIT_COMMUNITY_SEARCH_FALLBACK). Graph provenance is visible in graphEvidence field.',
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:16:} from '../lib/search/session-transition.js';
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:36:} from '../lib/search/recovery-payload.js';
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:45:} from '../lib/search/confidence-scoring.js';
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:52:} from '../lib/search/result-explainability.js';
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:71:/** Raw search result from database/vector search */
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:90:/** Formatted search result */
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:740:  searchType: string,
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:771:      tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:774:        searchType: searchType,
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:785:        'Try broadening your search query',
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:894:    // Prefer precomputed chunk reassembly from memory-search to avoid disk reads.
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:1074:    searchType: searchType,
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:1089:      searchType: _s,
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts:1101:    tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts:42:  | 'code_graph_query'
.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts:104:    case 'code_graph_query':
.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts:224:  //   recovery (0.20)      — A memory_context({ mode: "resume" }) call is the most
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/003-status-verification.md:28:- Prompt: `As a manual-testing orchestrator, check the CocoIndex Code status for this initialized project against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Output shows numeric file count > 0 and numeric chunk count > 0. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/003-status-verification.md:39:| CFG-003 | Status verification | Verify `ccc status` shows indexed file count and chunk count | `As a manual-testing orchestrator, check the CocoIndex Code status for this initialized project against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Output shows numeric file count > 0 and numeric chunk count > 0. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: ccc status` -> 2. Verify output contains file count and chunk count | Output shows numeric file count > 0 and numeric chunk count > 0 | Full `ccc status` output | PASS if both counts are present and non-zero; PARTIAL if only one count is visible but status still succeeds; FAIL if status command errors or shows zero counts | Run `ccc index` to populate index; check daemon connectivity; verify `.cocoindex_code/` exists |
.opencode/skills/system-spec-kit/mcp_server/lib/chunking/anchor-chunker.ts:63:/** Max characters for parent summary (BM25 fallback) */
.opencode/skills/system-spec-kit/mcp_server/hooks/README.md:104:- `MEMORY_AWARE_TOOLS` currently includes `memory_context`, `memory_search`, `memory_match_triggers`, `memory_list`, `memory_save`, and `memory_index_scan`.
.opencode/skills/system-spec-kit/mcp_server/formatters/token-metrics.ts:10:/** Tiered search result for token metric calculation */
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/001-default-model-verification.md:28:- Prompt: `As a manual-testing orchestrator, check the CocoIndex Code global settings for the embedding model against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Settings file exists; embedding.model matches a documented model such as the default local sentence-transformers/all-MiniLM-L6-v2 or a LiteLLM model like voyage/voyage-code-3. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/001-default-model-verification.md:39:| CFG-001 | Default model verification | Verify global settings contain the documented default embedding model | `As a manual-testing orchestrator, check the CocoIndex Code global settings for the embedding model against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Settings file exists; embedding.model matches a documented model such as the default local sentence-transformers/all-MiniLM-L6-v2 or a LiteLLM model like voyage/voyage-code-3. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: cat ~/.cocoindex_code/global_settings.yml` -> 2. Locate `embedding.provider` and `embedding.model` fields | Settings file exists; `embedding.model` matches a documented model such as `sentence-transformers/all-MiniLM-L6-v2` or `voyage/voyage-code-3` | Contents of `global_settings.yml` with embedding fields highlighted | PASS if embedding model field exists and matches a documented model; FAIL if file missing or model field absent | Check `COCOINDEX_CODE_DIR` env var; verify `~/.cocoindex_code/` directory exists; run `ccc init` if needed |
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-hierarchy.vitest.ts:14:} from '../lib/search/spec-folder-hierarchy';
.opencode/skills/mcp-coco-index/references/search_patterns.md:2:title: CocoIndex Code Search Patterns
.opencode/skills/mcp-coco-index/references/search_patterns.md:3:description: Effective semantic search strategies for getting the best results from CocoIndex Code, including query writing, filters, and when to choose semantic search over Grep.
.opencode/skills/mcp-coco-index/references/search_patterns.md:5:  - search strategies
.opencode/skills/mcp-coco-index/references/search_patterns.md:7:  - semantic search tips
.opencode/skills/mcp-coco-index/references/search_patterns.md:8:  - cocoindex search patterns
.opencode/skills/mcp-coco-index/references/search_patterns.md:9:  - when to use semantic search
.opencode/skills/mcp-coco-index/references/search_patterns.md:12:# CocoIndex Code Search Patterns
.opencode/skills/mcp-coco-index/references/search_patterns.md:14:Strategies for writing effective semantic queries and getting the best results from CocoIndex Code.
.opencode/skills/mcp-coco-index/references/search_patterns.md:21:Strategies and patterns for effective semantic code search using CocoIndex Code. Covers query writing, language and path filters, score interpretation, comparison with Grep, result verification workflows, and common query patterns by domain.
.opencode/skills/mcp-coco-index/references/search_patterns.md:29:Semantic search understands meaning, not just keywords. Write queries as you would describe what you are looking for to a colleague.
.opencode/skills/mcp-coco-index/references/search_patterns.md:62:Semantic search finds code by what it does, not how it looks.
.opencode/skills/mcp-coco-index/references/search_patterns.md:81:Filter by language when you know which language you need results from. CocoIndex Code supports **28+ languages** (see tool_reference.md for the full list).
.opencode/skills/mcp-coco-index/references/search_patterns.md:95:ccc search "database model definitions" --lang python
.opencode/skills/mcp-coco-index/references/search_patterns.md:98:ccc search "form validation component" --lang tsx
.opencode/skills/mcp-coco-index/references/search_patterns.md:101:ccc search "error handling and recovery" --lang go
.opencode/skills/mcp-coco-index/references/search_patterns.md:104:ccc search "table creation with foreign keys" --lang sql
.opencode/skills/mcp-coco-index/references/search_patterns.md:107:ccc search "authentication middleware" --lang python --lang typescript
.opencode/skills/mcp-coco-index/references/search_patterns.md:110:ccc search "data serialization" --lang python --lang rust --lang go
.opencode/skills/mcp-coco-index/references/search_patterns.md:113:**MCP equivalent:** The MCP `search` tool uses `languages` (a list of strings) instead of `--lang`:
.opencode/skills/mcp-coco-index/references/search_patterns.md:133:Scope searches to specific directories when you know where to look.
.opencode/skills/mcp-coco-index/references/search_patterns.md:139:ccc search "request validation" --path src/api/
.opencode/skills/mcp-coco-index/references/search_patterns.md:142:ccc search "mock database setup" --path tests/
.opencode/skills/mcp-coco-index/references/search_patterns.md:145:ccc search "user permissions" --path src/auth/
.opencode/skills/mcp-coco-index/references/search_patterns.md:148:ccc search "error handling" --path src/services/ --lang typescript
.opencode/skills/mcp-coco-index/references/search_patterns.md:149:ccc search "error handling" --path src/services/ --lang typescript --lang python
.opencode/skills/mcp-coco-index/references/search_patterns.md:169:ccc search "error handling with retry logic" --lang typescript --path src/api/ --limit 5
.opencode/skills/mcp-coco-index/references/search_patterns.md:172:ccc search "database integration test fixtures" --lang python --path tests/
.opencode/skills/mcp-coco-index/references/search_patterns.md:175:ccc search "memory allocation and deallocation" --lang rust --path src/core/
.opencode/skills/mcp-coco-index/references/search_patterns.md:177:# Multi-language search scoped to a directory
.opencode/skills/mcp-coco-index/references/search_patterns.md:178:ccc search "configuration loading" --lang python --lang typescript --path src/config/
.opencode/skills/mcp-coco-index/references/search_patterns.md:204:<!-- ANCHOR:semantic-search-vs-grep -->
.opencode/skills/mcp-coco-index/references/search_patterns.md:234:           YES --> Use CocoIndex Code (semantic)
.opencode/skills/mcp-coco-index/references/search_patterns.md:235:           NO  --> Use both: CocoIndex Code first to explore, then Grep to verify
.opencode/skills/mcp-coco-index/references/search_patterns.md:246:<!-- /ANCHOR:semantic-search-vs-grep -->
.opencode/skills/mcp-coco-index/references/search_patterns.md:250:Semantic search returns snippets. Always verify with the Read tool before acting on results.
.opencode/skills/mcp-coco-index/references/search_patterns.md:253:1. Run semantic search to find relevant files and locations
.opencode/skills/mcp-coco-index/references/search_patterns.md:260:ccc search "database connection setup"
.opencode/skills/mcp-coco-index/references/search_patterns.md:276:ccc search "how is the application structured"
.opencode/skills/mcp-coco-index/references/search_patterns.md:277:ccc search "entry point and initialization"
.opencode/skills/mcp-coco-index/references/search_patterns.md:278:ccc search "dependency injection setup"
.opencode/skills/mcp-coco-index/references/search_patterns.md:279:ccc search "module boundaries and exports"
.opencode/skills/mcp-coco-index/references/search_patterns.md:285:ccc search "error handling and recovery patterns"
.opencode/skills/mcp-coco-index/references/search_patterns.md:286:ccc search "custom error classes and types"
.opencode/skills/mcp-coco-index/references/search_patterns.md:287:ccc search "logging errors with context"
.opencode/skills/mcp-coco-index/references/search_patterns.md:288:ccc search "retry logic for failed operations"
.opencode/skills/mcp-coco-index/references/search_patterns.md:294:ccc search "database connection and pooling"
.opencode/skills/mcp-coco-index/references/search_patterns.md:295:ccc search "data validation before saving"
.opencode/skills/mcp-coco-index/references/search_patterns.md:296:ccc search "database migration scripts"
.opencode/skills/mcp-coco-index/references/search_patterns.md:297:ccc search "query optimization and indexing"
.opencode/skills/mcp-coco-index/references/search_patterns.md:303:ccc search "user authentication flow"
.opencode/skills/mcp-coco-index/references/search_patterns.md:304:ccc search "authorization and permissions"
.opencode/skills/mcp-coco-index/references/search_patterns.md:305:ccc search "password hashing and verification"
.opencode/skills/mcp-coco-index/references/search_patterns.md:306:ccc search "API key validation"
.opencode/skills/mcp-coco-index/references/search_patterns.md:312:ccc search "test setup and fixtures"
.opencode/skills/mcp-coco-index/references/search_patterns.md:313:ccc search "mocking external dependencies"
.opencode/skills/mcp-coco-index/references/search_patterns.md:314:ccc search "integration test configuration"
.opencode/skills/mcp-coco-index/references/search_patterns.md:315:ccc search "test data factories"
.opencode/skills/mcp-coco-index/references/search_patterns.md:321:ccc search "application configuration loading"
.opencode/skills/mcp-coco-index/references/search_patterns.md:322:ccc search "environment variable handling"
.opencode/skills/mcp-coco-index/references/search_patterns.md:323:ccc search "feature flags implementation"
.opencode/skills/mcp-coco-index/references/search_patterns.md:324:ccc search "configuration validation"
.opencode/skills/mcp-coco-index/references/search_patterns.md:337:| First query in session | Auto-refresh (if `refresh_index: true`) | `search` |
.opencode/skills/mcp-coco-index/references/search_patterns.md:348:# Safe: search without refreshing (recommended)
.opencode/skills/mcp-coco-index/references/search_patterns.md:349:ccc search "authentication flow"
.opencode/skills/mcp-coco-index/references/search_patterns.md:352:ccc search "authentication flow" --refresh-index
.opencode/skills/mcp-coco-index/references/search_patterns.md:357:When using `code_graph_context`, the response includes freshness metadata:
.opencode/skills/mcp-coco-index/references/search_patterns.md:365:Use `ccc_feedback` to improve search quality over time:
.opencode/skills/mcp-coco-index/references/search_patterns.md:371:Feedback is stored in `.opencode/skills/mcp-coco-index/feedback/search-feedback.jsonl` for analysis.
.opencode/skills/system-spec-kit/mcp_server/lib/chunking/README.md:118:| `PARENT_SUMMARY_LENGTH` | 500 chars | BM25 fallback summary extracted from file start |
.opencode/skills/system-spec-kit/mcp_server/lib/chunking/README.md:140:| [../search/README.md](../search/README.md) | Search pipeline that indexes chunked content |
.opencode/skills/system-spec-kit/mcp_server/lib/interfaces/README.md:82:| `IVectorStore` | `vector-store.ts` | Abstract base class for JS runtime consumers; subclasses must implement search/upsert/delete/get/stats/availability/dimension/close |
.opencode/skills/system-spec-kit/mcp_server/lib/interfaces/README.md:105:  async search(embedding, topK, options) { return []; }
.opencode/skills/system-spec-kit/mcp_server/lib/interfaces/README.md:122:await base.search([], 10); // throws: "Method search() must be implemented by subclass"
.opencode/skills/system-spec-kit/mcp_server/lib/interfaces/README.md:142:| [../search/vector-index-impl.ts](../search/vector-index-impl.ts) | Main in-repo `IVectorStore` implementation |
.opencode/skills/system-spec-kit/mcp_server/cli.ts:19:type VectorIndexModule = Awaited<typeof import('./lib/search/vector-index.js')>;
.opencode/skills/system-spec-kit/mcp_server/cli.ts:42:  return _vector_index ??= await import('./lib/search/vector-index.js');
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/002-project-settings-inspection.md:20:- Prompt: `As a manual-testing orchestrator, inspect the CocoIndex Code project settings for language coverage against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify include_patterns. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/002-project-settings-inspection.md:31:| CFG-002 | Project settings inspection | Verify project settings contain language extension patterns | `As a manual-testing orchestrator, inspect the CocoIndex Code project settings for language coverage against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify include_patterns. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: cat .cocoindex_code/settings.yml` -> 2. Locate `include_patterns` field -> 3. Count unique file extension patterns | `include_patterns` field present; contains patterns covering multiple language extensions (e.g., `*.py`, `*.ts`, `*.js`, `*.go`, `*.rs`, etc.) | Contents of `settings.yml` with include_patterns section; count of extension patterns | PASS if `include_patterns` contains patterns for 28+ language extensions (matching supported languages list); PARTIAL if patterns present but fewer than 28; FAIL if `include_patterns` missing | Run `ccc init -f` to regenerate defaults; compare against supported languages in tool_reference.md |
.opencode/skills/mcp-coco-index/references/settings_reference.md:2:title: CocoIndex Code Settings Reference
.opencode/skills/mcp-coco-index/references/settings_reference.md:12:# CocoIndex Code Settings Reference
.opencode/skills/mcp-coco-index/references/settings_reference.md:14:Complete reference for all CocoIndex Code configuration files, embedding model options, chunking parameters, and environment variables.
.opencode/skills/mcp-coco-index/references/settings_reference.md:126:| `voyage/voyage-code-3` | litellm | `VOYAGE_API_KEY` | 1024 | Best code search quality, recommended |
.opencode/skills/mcp-coco-index/references/settings_reference.md:144:CocoIndex Code splits source files into chunks for embedding and search. Chunking parameters are built-in and not user-configurable.
.opencode/skills/mcp-coco-index/references/settings_reference.md:151:| Algorithm          | RecursiveSplitter      | CocoIndex engine's recursive splitting algorithm |
.opencode/skills/mcp-coco-index/references/settings_reference.md:165:CocoIndex Code determines the project root using the following priority order:
.opencode/skills/mcp-coco-index/references/settings_reference.md:183:Running `ccc search "handler"` from `src/api/` finds `/home/user/projects/my-app/` as root (Priority 2: `.cocoindex_code/` found).
.opencode/skills/mcp-coco-index/references/settings_reference.md:226:| Search Patterns  | `.opencode/skills/mcp-coco-index/references/search_patterns.md` |
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation-bridge.vitest.ts:19:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation-bridge.vitest.ts:28:vi.mock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation-bridge.vitest.ts:47:vi.mock('../lib/search/encoding-intent', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation-bridge.vitest.ts:51:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation-bridge.vitest.ts:210:  it('keeps assistive high-similarity matches as a compatibility note in full-auto mode without archived BM25 cleanup side effects', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation-bridge.vitest.ts:332:  it('attempts BM25 repair for recon conflict stores in full-auto mode and surfaces the warning when repair fails', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation-bridge.vitest.ts:404:        'BM25 repair failed after recon conflict store for memory 901: repair conflict-store bm25 failure',
.opencode/skills/system-spec-kit/mcp_server/lib/interfaces/vector-store.ts:14:  async search(_embedding: unknown, _topK: number, _options?: unknown): Promise<unknown[]> {
.opencode/skills/system-spec-kit/mcp_server/lib/interfaces/vector-store.ts:15:    throw new Error('Method search() must be implemented by subclass');
.opencode/skills/system-spec-kit/mcp_server/hooks/codex/session-start.ts:95:        content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/skills/system-spec-kit/mcp_server/hooks/codex/session-start.ts:101:    content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/codex/session-start.ts:108:    content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/skills/mcp-coco-index/references/tool_reference.md:2:title: CocoIndex Code Tool Reference
.opencode/skills/mcp-coco-index/references/tool_reference.md:3:description: Complete reference for the CocoIndex Code CLI commands and MCP tool with parameters, examples, and expected output.
.opencode/skills/mcp-coco-index/references/tool_reference.md:7:  - search parameters
.opencode/skills/mcp-coco-index/references/tool_reference.md:12:# CocoIndex Code Tool Reference
.opencode/skills/mcp-coco-index/references/tool_reference.md:14:Complete reference for all CLI commands and the MCP tool exposed by CocoIndex Code.
.opencode/skills/mcp-coco-index/references/tool_reference.md:21:This document provides the complete reference for CocoIndex Code CLI commands and MCP tool. It covers all available commands (search, index, status, init, reset, mcp, daemon), their parameters, expected output, supported languages, environment variables, settings schema, and related resources.
.opencode/skills/mcp-coco-index/references/tool_reference.md:23:**Important distinction:** The MCP server exposes exactly **1 tool** (`search`). The `status`, `index`, and `reset` operations are **CLI-only commands** and are not available through the MCP protocol.
.opencode/skills/mcp-coco-index/references/tool_reference.md:31:### ccc search
.opencode/skills/mcp-coco-index/references/tool_reference.md:33:Perform a semantic search across the indexed codebase.
.opencode/skills/mcp-coco-index/references/tool_reference.md:36:ccc search QUERY [--lang LANG ...] [--path PATH] [--limit N] [--offset N] [--refresh]
.opencode/skills/mcp-coco-index/references/tool_reference.md:41:| `QUERY`     | Yes      | -       | Natural language search query                                      |
.opencode/skills/mcp-coco-index/references/tool_reference.md:46:| `--refresh` | No       | false   | Force index refresh before searching                               |
.opencode/skills/mcp-coco-index/references/tool_reference.md:52:# Basic search
.opencode/skills/mcp-coco-index/references/tool_reference.md:53:ccc search "error handling in API routes"
.opencode/skills/mcp-coco-index/references/tool_reference.md:56:ccc search "database connection pooling" --lang python
.opencode/skills/mcp-coco-index/references/tool_reference.md:59:ccc search "authentication middleware" --lang python --lang typescript
.opencode/skills/mcp-coco-index/references/tool_reference.md:62:ccc search "authentication middleware" --path src/api/
.opencode/skills/mcp-coco-index/references/tool_reference.md:65:ccc search "configuration" --limit 5 --offset 10
.opencode/skills/mcp-coco-index/references/tool_reference.md:67:# Refresh index before searching
.opencode/skills/mcp-coco-index/references/tool_reference.md:68:ccc search "new feature" --refresh
.opencode/skills/mcp-coco-index/references/tool_reference.md:78:> **Fork-specific telemetry.** This skill bundles a soft-fork of `cocoindex-code` (version `0.2.3+spec-kit-fork.0.2.0`) that adds dedup + path-class reranking. Result rows from `ccc search` carry additional fields (`dedupedAliases`, `uniqueResultCount`, `rankingSignals`, `source_realpath`, `content_hash`, `path_class`, `raw_score`) that vanilla upstream cocoindex-code does NOT emit. See [§7 Fork-Specific Output Telemetry](#-7-fork-specific-output-telemetry) for the full schema.
.opencode/skills/mcp-coco-index/references/tool_reference.md:105:- For forced refresh during search, use `ccc search ... --refresh`; the installed `ccc index` command does not expose a `--refresh` flag
.opencode/skills/mcp-coco-index/references/tool_reference.md:187:Run CocoIndex Code as an MCP server in stdio mode. Used by AI clients.
.opencode/skills/mcp-coco-index/references/tool_reference.md:200:- Exposes 1 tool: `search`
.opencode/skills/mcp-coco-index/references/tool_reference.md:237:The MCP server (`ccc mcp`) exposes exactly **1 tool**: `search`. All other operations (status, index, reset) are CLI-only commands.
.opencode/skills/mcp-coco-index/references/tool_reference.md:239:### search
.opencode/skills/mcp-coco-index/references/tool_reference.md:241:Perform semantic search across the indexed codebase.
.opencode/skills/mcp-coco-index/references/tool_reference.md:245:| `query`         | string                  | Yes      | -       | Natural language search query            |
.opencode/skills/mcp-coco-index/references/tool_reference.md:250:| `refresh_index` | boolean                 | No       | true    | Trigger index refresh before searching   |
.opencode/skills/mcp-coco-index/references/tool_reference.md:271:**Response:** Array of search results, each containing:
.opencode/skills/mcp-coco-index/references/tool_reference.md:293:| Index refresh before search | `--refresh` on `ccc search` | `refresh_index` | CLI search: default false. MCP: default true |
.opencode/skills/mcp-coco-index/references/tool_reference.md:301:CocoIndex Code supports **28+ programming and markup languages**:
.opencode/skills/mcp-coco-index/references/tool_reference.md:365:CocoIndex Code uses YAML settings files stored in the project `.cocoindex_code/` directory and the user home `~/.cocoindex_code/` directory.
.opencode/skills/mcp-coco-index/references/tool_reference.md:386:This skill bundles a vendored soft-fork of `cocoindex-code` (Python wrapper) at version `0.2.3+spec-kit-fork.0.2.0`. The fork ships REQ-001 through REQ-006 patches that add dedup, canonical path identity, path-class reranking, and ranking telemetry. All search responses (CLI `ccc search` and MCP `search` tool) include the fields below in addition to the standard `file` / `lines` / `snippet` / `score` / `language` baseline. **Vanilla upstream `cocoindex-code` 0.2.3 does NOT emit any of these fields.**
.opencode/skills/mcp-coco-index/references/tool_reference.md:396:| `path_class` | enum string | REQ-004 | Always after fork ≥0.2.0 reindex | One of: `implementation`, `tests`, `docs`, `spec_research`, `generated`, `vendor`. Drives the implementation-intent rerank in §7.3. |
.opencode/skills/mcp-coco-index/references/tool_reference.md:410:| `rankingSignals` | object | REQ-006 | Always on fork queries | Per-result breakdown of the score derivation. Keys include the path-class delta (`+0.05` for implementation matches on implementation-intent queries; `-0.05` for docs/spec_research matches), the dedup pre-grouping signal, and the raw vector similarity. Use this to debug "why did THIS result rank where it did". |
.opencode/skills/mcp-coco-index/references/tool_reference.md:417:- `path_class ∈ {docs, spec_research}` → score reduced by `-0.05`
.opencode/skills/mcp-coco-index/references/tool_reference.md:425:// MCP `search` response excerpt — note the extended fields beyond vanilla shape
.opencode/skills/mcp-coco-index/references/tool_reference.md:466:| Search Patterns  | `.opencode/skills/mcp-coco-index/references/search_patterns.md` |
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:4:// Converted from: search-results-format.test.ts (custom runner)
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:11:} from '../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:24:  searchType?: string;
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:253:  it('C10: Empty response includes search-broadening hints', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:377:  it('C12: searchType propagated to response data', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:381:    expect(envelope.data.searchType).toBe('multi-concept');
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:384:  it('C13: Response meta.tool is memory_search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts:388:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/001-query-intent-semantic-routing.md:16:- Objective: Verify that semantic queries (containing keywords like "find examples", "how to", "similar to", "explain") are classified as semantic and do not trigger structural graph augmentation in `memory_context`.
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/001-query-intent-semantic-routing.md:17:- Prompt: `As a manual-testing orchestrator, send a semantic query like "find examples of error handling patterns in this codebase" to memory_context against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Intent classified as 'semantic', routedBackend is semantic when present, no graphContext block in the response, no structural graph data injected into primary results. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/001-query-intent-semantic-routing.md:28:| INT-001 | Query-intent semantic routing | Semantic query stays on the semantic path, not the graph path | `Send "find examples of error handling patterns" to memory_context and verify semantic routing` | 1. `memory_context({ input: "find examples of error handling patterns in this codebase" })` | Intent classified as 'semantic', `queryIntentRouting.routedBackend` is `semantic` when present, no `graphContext` block | memory_context response showing routing metadata and semantic result shape | PASS if intent=semantic and no graph augmentation is injected; FAIL if structural routing or graphContext appears unexpectedly | Check SEMANTIC_KEYWORDS in query-intent-classifier.ts and graph augmentation guard in memory-context.ts |
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:2:title: CocoIndex Cross-CLI Playbook
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:3:description: Canonical AI operating guide for using CocoIndex safely and consistently across CLI environments.
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:12:# CocoIndex Cross-CLI Playbook
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:14:Canonical AI usage guide for CocoIndex across Claude, Gemini, Copilot, Codex, and OpenCode-style environments.
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:20:Use this reference when an agent or operator needs a stable, cross-CLI operating pattern for CocoIndex search, readiness checks, and troubleshooting. It captures the safe defaults that held up during the shared-repo hardening work:
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:23:- use CocoIndex for concept search and Grep for exact text
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:35:3. Use CocoIndex `search` for concept-based discovery.
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:78:5. Fall back to `Grep` if the task is exact-text search
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:86:| "How is auth implemented?" | CocoIndex | Semantic code discovery |
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:87:| "Where is retry logic?" | CocoIndex | Intent-based search |
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:88:| "Find all TODO comments" | Grep | Exact string search |
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:107:- MCP exposes only `search`.
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:112:- Do not assume sibling repos inherit CocoIndex from advisor heuristics alone. Downstream repos need the local skill payload plus `cocoindex_code` config wiring. See `references/downstream_adoption_checklist.md`.
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:117:- **MCP tool**: `mcp__cocoindex_code__search`
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:118:- **Auto-activation**: CLAUDE.md MANDATORY TOOLS says MUST use for concept search
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:119:- **Best practice**: Use MCP `search` tool directly; set `refresh_index=false` after first query
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:124:- **Best practice**: Use CLI `ccc search` via Bash or MCP `search` tool
.opencode/skills/mcp-coco-index/references/cross_cli_playbook.md:129:- **Best practice**: Combine with Google Search for external + CocoIndex for codebase context
.opencode/skills/system-spec-kit/mcp_server/tests/intent-routing.vitest.ts:8:} from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-routing.vitest.ts:9:import * as graphSearchFn from '../lib/search/graph-search-fn';
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:3:description: "This scenario validates that hybrid intent queries append structural graph context while the normal semantic retrieval payload remains intact."
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:10:This scenario validates that queries classified as `hybrid` by the query-intent classifier append code-graph context to the standard semantic retrieval response.
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:16:- Objective: Verify that hybrid queries (mixing structural keywords like "function", "calls" with semantic keywords like "explain", "examples") are classified as hybrid and append `graphContext` metadata to the normal `memory_context` response.
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:17:- Prompt: `As a manual-testing orchestrator, send a hybrid query like "find all validation functions and explain their error handling approach" to memory_context against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Intent classified as hybrid, response contains queryIntentRouting, graphContext appears when graph seeds resolve, and the normal semantic response body remains present. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:18:- Expected signals: Intent classified as `hybrid`, response contains `queryIntentRouting`, `graphContext` appears when graph seeds resolve, and the normal semantic response body remains present
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:19:- Pass/fail: PASS if hybrid routing is confirmed and graphContext is appended successfully; FAIL if graph augmentation is missing when expected or the response structure breaks
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:28:| INT-002 | Hybrid query result augmentation | Hybrid intent appends graphContext to the semantic response | `Send "find all validation functions and explain their error handling approach" to memory_context` | 1. `memory_context({ input: "find all validation functions and explain their error handling approach" })` | Intent classified as `hybrid`, `queryIntentRouting` present, `graphContext` appended when graph anchors resolve | memory_context response showing routing metadata plus graphContext | PASS if hybrid routing and graphContext augmentation are both present; FAIL if graph augmentation never appears when the graph has matching anchors | Check hybrid scoring threshold in query-intent-classifier.ts and graph augmentation path in memory-context.ts |
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md:45:- Feature file path: `07--code-graph-integration/002-hybrid-query-merges-results.md`
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:2:title: CocoIndex Downstream Adoption Checklist
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:3:description: Minimum rollout checklist for enabling CocoIndex in a sibling repo without adding new routing rules or hidden config-writing automation.
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:11:# CocoIndex Downstream Adoption Checklist
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:13:Minimum rollout checklist for enabling CocoIndex in a sibling repo.
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:19:Use this checklist when a sibling repo needs real CocoIndex adoption instead of advisor-only heuristics. The key rule is that downstream rollout is a three-layer contract:
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:51:If this payload is missing, `skill_advisor.py` cannot discover `mcp-coco-index` even if semantic-search heuristics exist.
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:70:Barter already has advisor-side CocoIndex logic, but it still lacks:
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:75:That means the advisor can attempt semantic behavior, but it still cannot recommend or use the CocoIndex skill there end to end.
.opencode/skills/mcp-coco-index/references/downstream_adoption_checklist.md:115:- the local CocoIndex skill payload exists
.opencode/skills/system-spec-kit/mcp_server/lib/storage/schema-downgrade.ts:137:      context_type TEXT DEFAULT 'general' CHECK(context_type IN ('research', 'implementation', 'planning', 'general')), -- P1-5: canonical-only (legacy values migrated by v25)
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/custom-instructions.ts:35:const STARTUP_FALLBACK = 'Startup context unavailable. Call `session_bootstrap()` or `memory_context({ mode: "resume", profile: "resume" })` if more context is needed.';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:6:import { createUnifiedGraphSearchFn, computeDegreeScores, clearDegreeCache } from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:90:    // Default: FTS table not available so fallback path is used
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:99:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:100:    const results = searchFn('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:111:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:112:    const results = searchFn('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:122:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:123:    const results = searchFn('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:136:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:137:    const results = searchFn('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:148:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:149:    const results = searchFn('memory', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:164:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:165:    const results = searchFn('memory', { limit: 20 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:180:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:181:    const results = searchFn('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:191:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:192:    const results = searchFn('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:204:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:205:    searchFn('spec', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:218:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:219:    expect(searchFn('memory', { limit: 10 })).toEqual([]);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:239:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:240:    const results = searchFn('memory', { limit: 5, specFolder: '003-root/007-child' });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:246:  it('preserves BM25-aware composite scores in the FTS5 path', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:253:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:254:    const results = searchFn('memory', { limit: 20 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:262:  it('deduplicates FTS results using the highest composite score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:269:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:270:    const results = searchFn('memory', { limit: 20 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:284:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:285:    const results = searchFn('memory', { limit: 20 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-search-fn.vitest.ts:323:        hybridSearch: { init: vi.fn() },
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:7:import * as vectorIndex from '../../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:8:import * as bm25Index from '../../lib/search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:22:import { classifyEncodingIntent } from '../../lib/search/encoding-intent.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:23:import { isEncodingIntentEnabled } from '../../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:262: * Creates a memory row with metadata, optional BM25 entry, and save history.
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:410:          ? `[memory-save] BM25 indexing failed: ${message}`
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:411:          : `[memory-save] BM25 indexing failed (deferred path): ${message}`);
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:2:title: "INT-003 -- Session recovery surfaces include CocoIndex availability status"
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:3:description: "This scenario validates that session_bootstrap and session_resume expose CocoIndex availability in the integrated recovery flow."
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:6:# INT-003 -- Session recovery surfaces include CocoIndex availability status
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:10:This scenario validates that the integrated recovery flow exposes CocoIndex availability correctly. `session_bootstrap` is the canonical first-call recovery surface and should carry CocoIndex status inside `resume`. `session_resume` remains the detailed follow-up surface and should still expose the direct `cocoIndex` field alongside memory context and code graph status.
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:16:- Objective: Verify that `session_bootstrap` exposes CocoIndex status through `resume.cocoIndex`, that `session_resume` still exposes the direct `cocoIndex` field, and that both surfaces degrade gracefully when the CocoIndex binary is unavailable. `available` reflects whether the `ccc` binary exists at the expected install path, not whether the daemon is currently running. The `binaryPath` must point to the expected `ccc` binary location.
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:17:- Prompt: `As a manual-testing orchestrator, call session_bootstrap and session_resume, then examine the CocoIndex status fields against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify session_bootstrap.resume.cocoIndex.available and session_resume.cocoIndex.available match binary presence on disk; both binaryPath values are non-empty strings; session_bootstrap includes structuralContext; both calls complete without error regardless of binary availability. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:19:- Pass/fail: PASS if both recovery surfaces expose the expected CocoIndex fields with correct types and availability matches binary presence; FAIL if either field is missing, wrong type, or either recovery call crashes when the binary is unavailable
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:28:| INT-003a | Session bootstrap CocoIndex status | Canonical first-call recovery includes CocoIndex status | `Call session_bootstrap with CocoIndex installed` | 1. `test -x .opencode/skills/mcp-coco-index/mcp_server/.venv/bin/ccc` 2. `session_bootstrap({})` via MCP | `resume.cocoIndex.available === true`, `resume.cocoIndex.binaryPath` is non-empty, `structuralContext` present | session_bootstrap response JSON resume.cocoIndex + structuralContext | PASS if bootstrap exposes cocoIndex and structuralContext correctly; FAIL if either field is missing while the binary is present | Check session-bootstrap.ts + session-resume.ts integration and session-snapshot contract |
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:29:| INT-003b | Session resume CocoIndex status | Detailed recovery surface preserves direct CocoIndex field | `Call session_resume with CocoIndex installed` | 1. `test -x .opencode/skills/mcp-coco-index/mcp_server/.venv/bin/ccc` 2. `session_resume({})` via MCP | `cocoIndex.available === true`, `binaryPath` is non-empty string | session_resume response JSON cocoIndex field | PASS if direct resume surface still exposes cocoIndex fields; FAIL if fields are missing while the binary is present | Check ccc binary path handling in session-resume.ts and `cocoindex-path.ts` |
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md:30:| INT-003c | Recovery surfaces degrade gracefully without CocoIndex | Bootstrap and resume succeed when CocoIndex binary is absent | 1. Run in a disposable environment where `.opencode/skills/mcp-coco-index/mcp_server/.venv/bin/ccc` is absent 2. `session_bootstrap({})` via MCP 3. `session_resume({})` via MCP | Both responses succeed; availability fields become `false`; hints may include recovery/install guidance | session_bootstrap + session_resume response JSON showing graceful degradation | PASS if both calls succeed with `available=false`; FAIL if either call throws or the availability field is missing | Check error handling in the CocoIndex availability probe plus `cocoindex-path.ts` |
.opencode/skills/mcp-coco-index/changelog/CHANGELOG.md:15:- `path_class` chunk field with implementation/tests/docs/spec_research/generated/vendor taxonomy (REQ-004)
.opencode/skills/mcp-coco-index/changelog/CHANGELOG.md:17:- Bounded path-class reranking for implementation-intent queries (+0.05 implementation, -0.05 docs/spec_research) (REQ-005)
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:102:    '- CocoIndex: unknown',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:126:      'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:136:      'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:147:      'Context was compacted, but the cached compact brief was quarantined by semantic validation. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/copilot/session-prime.ts:164:    'Context was compacted and auto-recovered from the cached compact brief. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/skills/system-spec-kit/mcp_server/lib/validation/README.md:263:  findSimilar: (emb, opts) => vectorStore.search(emb, opts),
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:4:import * as handler from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:7:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:59:    it('T516-2: handle_memory_search alias is exported', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:60:      expect(typeof handler.handle_memory_search).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:178:            title: 'Healthy FTS result',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts:228:      query: 'canonical continuity search',
.opencode/skills/system-spec-kit/mcp_server/lib/storage/access-tracker.ts:223: * Calculate usage boost for search ranking.
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:62:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:73:      content: 'Context was compacted. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:85:      content: 'Context was compacted, but the cached compact brief was quarantined by semantic validation. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:103:      content: 'Context was compacted and auto-recovered from the cached compact brief. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:172:    '- CocoIndex: unknown',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:248:        '- `memory_context({ input, mode })` — unified context retrieval',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:249:        '- `memory_match_triggers({ prompt })` — fast trigger matching',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:250:        '- `memory_search({ query })` — semantic search',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:251:        '- `code_graph_scan`, `code_graph_query`, `code_graph_context`, `code_graph_status`',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:306:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:311:      content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/session-prime.ts:323:      content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/skills/system-spec-kit/mcp_server/lib/learning/corrections.ts:7:import { clearDegreeCacheForDb } from '../search/graph-search-fn.js';
.opencode/skills/mcp-coco-index/graph-metadata.json:12:        "context": "semantic search for spec context"
.opencode/skills/mcp-coco-index/graph-metadata.json:21:        "context": "semantic search boosts advisor discovery routing"
.opencode/skills/mcp-coco-index/graph-metadata.json:26:    "code-search",
.opencode/skills/mcp-coco-index/graph-metadata.json:27:    "semantic-search",
.opencode/skills/mcp-coco-index/graph-metadata.json:32:    "semantic search",
.opencode/skills/mcp-coco-index/graph-metadata.json:33:    "code search",
.opencode/skills/mcp-coco-index/graph-metadata.json:39:      "semantic search",
.opencode/skills/mcp-coco-index/graph-metadata.json:40:      "code search",
.opencode/skills/mcp-coco-index/graph-metadata.json:43:      "semantic code search",
.opencode/skills/mcp-coco-index/graph-metadata.json:45:      "cocoindex code search",
.opencode/skills/mcp-coco-index/graph-metadata.json:50:      "semantic-search"
.opencode/skills/mcp-coco-index/graph-metadata.json:53:      "code-search",
.opencode/skills/mcp-coco-index/graph-metadata.json:54:      "semantic-search",
.opencode/skills/mcp-coco-index/graph-metadata.json:57:      "semantic code search",
.opencode/skills/mcp-coco-index/graph-metadata.json:60:      "mcp search tool",
.opencode/skills/mcp-coco-index/graph-metadata.json:67:      ".opencode/skills/mcp-coco-index/references/search_patterns.md",
.opencode/skills/mcp-coco-index/graph-metadata.json:87:        "name": "search_patterns",
.opencode/skills/mcp-coco-index/graph-metadata.json:89:        "path": ".opencode/skills/mcp-coco-index/references/search_patterns.md",
.opencode/skills/mcp-coco-index/graph-metadata.json:117:    "causal_summary": "Semantic code search via vector embeddings. CocoIndex Code enables natural-language discovery of relevant code, patterns, and implementations. CLI for direct use; MCP exposes a single `search` tool for AI agent integration. It matters because it provides the semantic search layer that finds relevant code by concept instead of exact token matching.",
.opencode/skills/mcp-coco-index/graph-metadata.json:121:      "references/search_patterns.md",
.opencode/skills/system-spec-kit/mcp_server/handlers/save/types.ts:7:import type { SavePlannerMode } from '../../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/types.ts:114: * filter or overfetch window dropped otherwise-relevant vector-search
.opencode/skills/system-spec-kit/mcp_server/handlers/save/types.ts:225:  | 'research_finding'
.opencode/skills/system-spec-kit/mcp_server/lib/storage/consolidation.ts:8:import { isConsolidationEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:151:  research: 'research_findings',
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:152:  research_findings: 'research_findings',
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:187:    { basename: 'research.md', path: path.join(folder, 'research.md') },
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:188:    { basename: 'research/research.md', path: path.join(folder, 'research', 'research.md') },
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:753:        return shape === 'section' || /research/.test(path.basename(targetPath));
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:847:    if (/research(?:\/research)?\.md$/.test(document.basename)) {
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:848:      const citedResearch = parsed.anchors.some((anchor) => looksLikeCitation(anchor.body));
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:849:      if (!citedResearch) {
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:853:          detail: `${document.basename}: research content is missing a citation`,
.opencode/skills/system-spec-kit/mcp_server/lib/validation/spec-doc-structure.ts:896:    return 'research_findings';
.opencode/skills/mcp-coco-index/LICENSE:189:   Copyright 2026 CocoIndex Inc
.opencode/skills/system-spec-kit/mcp_server/tests/session-health.vitest.ts:68:    recommendedAction: 'Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/tests/session-health.vitest.ts:112:    currentSpecFolder: 'system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research',
.opencode/skills/system-spec-kit/mcp_server/handlers/save/README.md:45:| `create-record.ts`          | Core record creation. Inserts into vector index (or deferred index), applies post-insert metadata, links related memories and indexes into BM25 when enabled. |
.opencode/skills/system-spec-kit/mcp_server/handlers/save/README.md:60:6. create-record  -- Insert memory into vector + BM25 indexes
.opencode/skills/system-spec-kit/mcp_server/handlers/save/README.md:74:- **Deferred Indexing** -- When embedding generation fails or async mode is explicitly requested, the spec-doc record is stored with `embedding_status = 'pending'` and remains searchable via BM25/FTS5. Normal watcher/ingest reindex cache misses still run the eager provider path.
.opencode/skills/system-spec-kit/mcp_server/handlers/save/README.md:88:- `../../lib/search/vector-index.ts` -- vector index operations
.opencode/skills/system-spec-kit/mcp_server/handlers/save/README.md:89:- `../../lib/search/bm25-index.ts` -- BM25 full-text index
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/003-language-filter-multi.md:20:- Prompt: `As a manual-testing orchestrator, search CocoIndex for "function" in both Python and JavaScript against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results contain mix of .py and .js files; no other extensions. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/003-language-filter-multi.md:31:| MCP-003 | Language filter (multi) | Verify `languages` parameter accepts multiple languages | `As a manual-testing orchestrator, search CocoIndex for "function" in both Python and JavaScript against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results contain mix of .py and .js files; no other extensions. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "function definition", "languages": ["python", "javascript"] })` -> 2. Verify returned files are `.py` or `.js`/`.mjs`/`.cjs` only | Results contain mix of `.py` and `.js` files; no other extensions | MCP output with file extensions annotated | PASS if all results are Python or JavaScript files AND at least one of each appears; PARTIAL if all results are one language only but correct; FAIL if wrong language appears | Check language code values (use "python", "javascript"); verify index has both file types |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/003-language-filter-multi.md:48:- Feature file path: `02--mcp-search-tool/003-language-filter-multi.md`
.opencode/skills/system-spec-kit/mcp_server/lib/validation/save-quality-gate.ts:21:import { isSaveQualityGateEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/validation/save-quality-gate.ts:22:import * as vectorIndex from '../search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/validation/save-quality-gate.ts:694: * @param specFolder - The spec folder to search within
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/README.md:54:Hooks are transport reliability, not separate business logic. They call the same retrieval primitives (`memory_match_triggers`, `memory_context`) that other runtimes call explicitly.
.opencode/skills/system-spec-kit/mcp_server/tests/unit-normalization.vitest.ts:130:      spec_folder: 'specs/010-search',
.opencode/skills/system-spec-kit/mcp_server/tests/unit-normalization.vitest.ts:131:      file_path: 'specs/010-search/memory/ctx-001.md',
.opencode/skills/system-spec-kit/mcp_server/tests/unit-normalization.vitest.ts:138:    expect(memory.specFolder).toBe('specs/010-search');
.opencode/skills/system-spec-kit/mcp_server/tests/unit-normalization.vitest.ts:139:    expect(memory.filePath).toBe('specs/010-search/memory/ctx-001.md');
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:14:This scenario validates concurrent-search behavior under `refresh_index=true` for `MCP-008`. SKILL.md §4 ("Concurrent Query Sessions") documents that the daemon has a known concurrency issue where simultaneous `refresh_index=true` requests can cause `ComponentContext` errors and instructs operators to set `refresh_index=false` after the first session query. This scenario gives that warning a deterministic test.
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:27:- Real user request: `"Run two CocoIndex searches at the same time and tell me whether the refresh-index race is real."`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:28:- Prompt: `As a manual-testing orchestrator, fire two MCP CocoIndex searches concurrently with refresh_index=true against the current CocoIndex daemon in this repository. Verify either both responses are valid result arrays OR at least one response surfaces a ComponentContext error string (acceptable failure mode per SKILL.md §4). Confirm that switching the second call to refresh_index=false eliminates the error. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:29:- Expected execution process: dispatch two MCP `search` calls in the same shell using background subprocesses or two parallel tool invocations; collect both responses; inspect for `ComponentContext` substring; rerun second call with `refresh_index=false` to confirm clean path.
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:40:- Prompt: `As a manual-testing orchestrator, fire two MCP CocoIndex searches concurrently with refresh_index=true against the current CocoIndex daemon in this repository. Verify either both responses are valid result arrays OR at least one response surfaces a ComponentContext error string (acceptable failure mode per SKILL.md §4). Confirm that switching the second call to refresh_index=false eliminates the error. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:46:   - Call A: `mcp__cocoindex_code__search({ "query": "error handling", "refresh_index": true, "limit": 3 })`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:47:   - Call B: `mcp__cocoindex_code__search({ "query": "configuration loader", "refresh_index": true, "limit": 3 })`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:49:4. `mcp__cocoindex_code__search({ "query": "configuration loader", "refresh_index": false, "limit": 3 })` — confirm the recommended fallback path returns results
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:90:| `02--mcp-search-tool/007-no-refresh-search.md` | Sibling scenario covering the `refresh_index=false` happy path |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md:107:- Feature file path: `02--mcp-search-tool/008-concurrent-refresh-race.md`
.opencode/skills/system-spec-kit/mcp_server/lib/config/README.md:42:| **10 Spec Document Types** | `spec`, `plan`, `tasks`, `checklist`, `decision_record`, `implementation_summary`, `research`, `handover`, `description_json`, `graph_metadata` |
.opencode/skills/system-spec-kit/mcp_server/lib/config/README.md:236:| [../../configs/search-weights.json](../../configs/search-weights.json) | Runtime weight configuration |
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:66:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:77:      content: 'Context was compressed. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:89:      content: 'Context was compressed, but the cached compact brief was quarantined by semantic validation. Call `memory_context({ mode: "resume", profile: "resume" })` to recover session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:106:      content: 'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:180:        '- CocoIndex: unknown',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:188:        '- `memory_context({ input, mode })` - unified context retrieval',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:189:        '- `memory_match_triggers({ prompt })` - fast trigger matching',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:190:        '- `memory_search({ query })` - semantic search',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:191:        '- `code_graph_scan`, `code_graph_query`, `code_graph_context`, `code_graph_status`',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:239:      content: `Last active spec folder: ${state.lastSpecFolder}\nCall \`memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })\` for full context.`,
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:245:    content: 'Call `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` to restore session state.',
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/session-prime.ts:253:    content: 'Session cleared. Spec Kit Memory is active. Use `memory_context` or `memory_match_triggers` to load relevant context.',
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:7:import * as vectorIndex from '../../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:9:import * as bm25Index from '../../lib/search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:14:import { classifyEncodingIntent } from '../../lib/search/encoding-intent.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:19:} from '../../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:20:import type { SavePlannerMode } from '../../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:65:   * T-RCB-10 (R16-002): vector-search rows rejected as malformed — missing
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:72:   * T-RCB-09 (R12-003): original vector-search row count before scope/malformed
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:224:    console.warn(`[memory-save] Immediate BM25 repair failed (${args.contextLabel}): ${repairMessage}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:225:    return `BM25 repair failed after ${args.contextLabel} for memory ${args.memoryId}: ${repairMessage}`;
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:295: * T-RCB-10 (R16-002): reject malformed vector-search rows instead of coercing
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:417:  searchResult: ScopeFilteredSearchResult,
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:421:  const { candidates, suppressedCandidateIds, malformedCandidateCount, rawCandidateCount } = searchResult;
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:446:      `[memory-save] ${contextLabel}: rejected ${malformedCandidateCount} malformed vector-search row(s).`,
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:506:  // T-04: search-flags.ts is the canonical caller-visible opt-in gate.
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:538:                const searchEmb = emb instanceof Float32Array ? emb : new Float32Array(emb as number[]);
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:539:                const searchResult = findScopeFilteredCandidates({
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:541:                  embedding: searchEmb,
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:551:                  searchResult,
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:555:                return searchResult.candidates;
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:570:              // P1-01 fix — wrap all DB writes (index, metadata, BM25, history) in a
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:620:                    console.warn(`[memory-save] BM25 indexing failed (recon conflict store): ${message}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:649:          const warning = `TM-06: Reconsolidation similarity search failed: ${similarityFailureMessage}`;
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:778:      // Find the top similar memory using the existing vector search
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:779:      const searchEmb = embedding instanceof Float32Array ? embedding : new Float32Array(embedding as number[]);
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts:782:        embedding: searchEmb,
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/004-path-filter.md:20:- Prompt: `As a manual-testing orchestrator, search CocoIndex for "skill" only under .opencode/skills/ against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify All result paths begin with .opencode/skills/; no results from other directories. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/004-path-filter.md:31:| MCP-004 | Path filter | Verify `paths` parameter restricts results to a specific directory | `As a manual-testing orchestrator, search CocoIndex for "skill" only under .opencode/skills/ against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify All result paths begin with .opencode/skills/; no results from other directories. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "skill configuration", "paths": [".opencode/skills/"] })` -> 2. Verify all returned file paths start with `.opencode/skills/` | All result paths begin with `.opencode/skills/`; no results from other directories | MCP output with file paths | PASS if all results are under `.opencode/skills/`; FAIL if any result is outside that path | Verify path format (relative, with trailing slash); check if path is indexed |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/004-path-filter.md:48:- Feature file path: `02--mcp-search-tool/004-path-filter.md`
.opencode/skills/system-spec-kit/mcp_server/lib/storage/README.md:39:- The primary memory schema is at `SCHEMA_VERSION = 23` in `lib/search/vector-index-schema.ts`.
.opencode/skills/system-spec-kit/mcp_server/lib/storage/README.md:55:| `learned-triggers-schema.ts` | Migration helpers for the `learned_triggers` column and FTS isolation checks |
.opencode/skills/system-spec-kit/mcp_server/lib/storage/README.md:80:- `../search/README.md`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/002-language-filter-single.md:20:- Prompt: `As a manual-testing orchestrator, search CocoIndex for "function" filtered to Python only against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify All result file paths end in .py; no .ts, .js, .go, etc. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/002-language-filter-single.md:31:| MCP-002 | Language filter (single) | Verify `languages` parameter restricts results to a single language | `As a manual-testing orchestrator, search CocoIndex for "function" filtered to Python only against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify All result file paths end in .py; no .ts, .js, .go, etc. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "function definition", "languages": ["python"] })` -> 2. Verify all returned `file` paths end in `.py` | All result file paths end in `.py`; no `.ts`, `.js`, `.go`, etc. | MCP output with file paths highlighted | PASS if all results are `.py` files; FAIL if any non-Python file appears | Verify `languages` parameter accepts list format; check index has Python files with `ccc status` |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/002-language-filter-single.md:48:- Feature file path: `02--mcp-search-tool/002-language-filter-single.md`
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:78:  '/spec_kit:deep-research': [['sk-deep-research', 1.6], ['command-spec-kit', 0.45]],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:98:  'deep research': [['sk-deep-research', 1]],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:100:  'deep-research': [['sk-deep-research', 1.3]],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:114:  'resume deep research': [['sk-deep-research', 1]],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:126:  'semantic code search': [['mcp-coco-index', 1]],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:132:  'vector-search': [['mcp-coco-index', 1]],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:171:  if (/\b(continue|resume|launch|kick off|overnight|convergence|iteration)\b/.test(lower) && /\bresearch\b/.test(lower)) {
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/explicit.ts:172:    push(scores, 'sk-deep-research', 0.85, 'research-loop');
.opencode/skills/system-spec-kit/mcp_server/lib/config/memory-types.ts:151:  { pattern: /\/research\/iterations\//, type: 'working' },
.opencode/skills/system-spec-kit/mcp_server/lib/config/memory-types.ts:374:  | 'research'
.opencode/skills/system-spec-kit/mcp_server/lib/config/memory-types.ts:401:  { filePattern: /(?:^|\/)(?:research\/research\.md|research\.md)$/i, documentType: 'research', memoryType: 'semantic', defaultImportanceTier: 'normal', defaultImportanceWeight: 0.6 },
.opencode/skills/system-spec-kit/mcp_server/lib/config/memory-types.ts:422:    research: 'research.md',
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:2:title: "MCP-001 -- Basic semantic search"
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:3:description: "This scenario validates Basic semantic search for `MCP-001`. It focuses on Verify MCP search returns results with file paths, scores, and line ranges."
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:6:# MCP-001 -- Basic semantic search
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:10:This scenario validates Basic semantic search for `MCP-001`. It focuses on Verify MCP search returns results with file paths, scores, and line ranges.
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:19:- Objective: Verify MCP search returns results with file paths, scores, and line ranges
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:20:- Prompt: `As a manual-testing orchestrator, use CocoIndex to search for "fibonacci calculation" against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results array with at least 1 entry; each entry contains file (string), score (float 0.0-1.0), lines (start/end), snippet (string), language (string). Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:31:| MCP-001 | Basic semantic search | Verify MCP search returns results with file paths, scores, and line ranges | `As a manual-testing orchestrator, use CocoIndex to search for "fibonacci calculation" against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results array with at least 1 entry; each entry contains file (string), score (float 0.0-1.0), lines (start/end), snippet (string), language (string). Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "fibonacci calculation" })` | Results array with at least 1 entry; each entry contains `file` (string), `score` (float 0.0-1.0), `lines` (start/end), `snippet` (string), `language` (string) | MCP tool output showing result structure | PASS if results non-empty AND each result has all 5 fields (file, score, lines, snippet, language); FAIL if empty results or missing fields | Check index status with `ccc status`; verify index is non-empty; try broader query like "math calculation" |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md:48:- Feature file path: `02--mcp-search-tool/001-basic-semantic-search.md`
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:3:import type { Stage2Input } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:19:vi.mock('../lib/search/learned-feedback', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:44:vi.mock('../lib/search/session-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:48:vi.mock('../lib/search/causal-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:52:vi.mock('../lib/search/anchor-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:56:vi.mock('../lib/search/validation-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:64:      searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:72:      searchType: 'vector' as const,
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:135:    const { __testables } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:158:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:190:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:213:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:253:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:284:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:314:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:338:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:361:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:381:    vi.doMock('../lib/search/session-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:388:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:392:    input.config.searchType = 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:401:    vi.doMock('../lib/search/causal-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:408:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:412:    input.config.searchType = 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:420:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2-fusion.vitest.ts:424:    input.config.searchType = 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:6:// using the 3-source merge pipeline (Memory, Code Graph, CocoIndex)
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:151:  // Hint for AI to use CocoIndex for semantic neighbors after recovery
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:153:    sections.push('## Semantic Context (CocoIndex)\nUse `mcp__cocoindex_code__search` to find semantic neighbors of active files listed above.');
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:229:    ? 'Use `mcp__cocoindex_code__search` to find semantic neighbors of active files listed above.'
.opencode/skills/system-spec-kit/mcp_server/hooks/claude/compact-inject.ts:365:      ? 'Use `mcp__cocoindex_code__search` to find semantic neighbors of active files listed above.'
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/005-combined-filters.md:28:- Prompt: `As a manual-testing orchestrator, search CocoIndex for "config" in Python under .opencode/ with 2 results against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Result count <= 2; all files are .py; all paths start with .opencode/. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/005-combined-filters.md:39:| MCP-005 | Combined filters | Verify `languages`, `paths`, and `limit` work together | `As a manual-testing orchestrator, search CocoIndex for "config" in Python under .opencode/ with 2 results against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Result count <= 2; all files are .py; all paths start with .opencode/. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "configuration loading", "languages": ["python"], "paths": [".opencode/"], "limit": 2 })` -> 2. Verify results are Python files under `.opencode/` and count <= 2 | Result count <= 2; all files are `.py`; all paths start with `.opencode/` | MCP output showing filtered results | PASS if count <= 2 AND all filters satisfied; FAIL if any filter is ignored | Test filters individually to isolate which one fails; check parameter types (list vs string) |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/005-combined-filters.md:56:- Feature file path: `02--mcp-search-tool/005-combined-filters.md`
.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:9:import * as bm25Index from '../search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:13:import { ensureLineageTables } from '../search/vector-index-schema.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:14:import { get_embedding_dim, refresh_interference_scores_for_folder, sqlite_vec_available } from '../search/vector-index-store.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:15:import { to_embedding_buffer } from '../search/vector-index-types.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:17:import { classifyEncodingIntent } from '../search/encoding-intent.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:18:import { isEncodingIntentEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:529:      logger.warn(`BM25 index update failed for memory ${memoryId}: ${error instanceof Error ? error.message : String(error)}`);
.opencode/skills/system-spec-kit/mcp_server/tests/ground-truth-feedback.vitest.ts:58:        searchMode: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/ground-truth-feedback.vitest.ts:84:        searchMode: 'context',
.opencode/skills/system-spec-kit/mcp_server/tests/ground-truth-feedback.vitest.ts:137:        searchMode: 'trigger',
.opencode/skills/system-spec-kit/mcp_server/tests/ground-truth-feedback.vitest.ts:151:      expect(sel.context.searchMode).toBe('trigger');
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md:3:description: "This scenario validates Semantic flag routing for `ADV-001`. It focuses on Verify `--semantic` triggers CocoIndex search and `!semantic(...)` appears in reason field when skill references found."
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md:10:This scenario validates Semantic flag routing for `ADV-001`. It focuses on Verify `--semantic` triggers CocoIndex search and `!semantic(...)` appears in reason field when skill references found.
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md:19:- Objective: Verify `--semantic` triggers CocoIndex search and `!semantic(...)` appears in reason field when skill references found
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md:20:- Prompt: `As a manual-testing orchestrator, test skill advisor with semantic search for a deployment query against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify JSON output is valid; at least one recommendation entry contains !semantic( in its reason field; CocoIndex search was invoked (visible in processing or reason text). Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md:21:- Expected signals: JSON output is valid; at least one recommendation entry contains `!semantic(` in its `reason` field; CocoIndex search was invoked (visible in processing or reason text)
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md:22:- Pass/fail: PASS if valid JSON returned AND at least one `reason` contains `!semantic(`; PARTIAL if JSON valid but no `!semantic` (CocoIndex may not have found skill refs); FAIL if command errors or invalid JSON
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md:31:| ADV-001 | Semantic flag routing | Verify `--semantic` triggers CocoIndex search and `!semantic(...)` appears in reason field when skill references found | `As a manual-testing orchestrator, test skill advisor with semantic search for a deployment query against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify JSON output is valid; at least one recommendation entry contains !semantic( in its reason field; CocoIndex search was invoked (visible in processing or reason text). Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: python3 .opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py "deploy to production" --semantic --show-rejections` -> 2. Inspect JSON output for `reason` fields containing `!semantic(...)` notation | JSON output is valid; at least one recommendation entry contains `!semantic(` in its `reason` field; CocoIndex search was invoked (visible in processing or reason text) | Full JSON output of skill_advisor.py; highlighted `reason` fields with `!semantic` notation | PASS if valid JSON returned AND at least one `reason` contains `!semantic(`; PARTIAL if JSON valid but no `!semantic` (CocoIndex may not have found skill refs); FAIL if command errors or invalid JSON | Verify `ccc` binary is on PATH (required for `--semantic`); check daemon is running; try `ccc search "deploy" --limit 3` directly to confirm CocoIndex works |
.opencode/skills/system-spec-kit/mcp_server/lib/config/type-inference.ts:171:  // Build searchable text from title and triggers
.opencode/skills/system-spec-kit/mcp_server/lib/config/type-inference.ts:172:  const searchableText = [
.opencode/skills/system-spec-kit/mcp_server/lib/config/type-inference.ts:181:  // Combined text for searching
.opencode/skills/system-spec-kit/mcp_server/lib/config/type-inference.ts:182:  const fullText = `${searchableText} ${contextType}`;
.opencode/skills/system-spec-kit/mcp_server/handlers/save/markdown-evidence-builder.ts:118:    if (/^(?:feature|implementation|observation|read|write|edit|bash|grep|glob|search|tool)\s*:/.test(heading)) {
.opencode/skills/system-spec-kit/mcp_server/tests/retry-manager.vitest.ts:8:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:18:import * as bm25Index from '../search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:19:import { clear_search_cache } from '../search/vector-index-aliases.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:20:import { refresh_interference_scores_for_folder } from '../search/vector-index-store.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:23:import { delete_memory_from_database } from '../search/vector-index-mutations.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:40:/** An existing memory found during similarity search */
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:159:// Reconsolidation gate — canonical implementation in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:161:import { isReconsolidationEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:172: * @param specFolder - The spec folder to search within
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:374:          console.warn('[reconsolidation] Failed to update BM25 index for merge:', message);
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:380:      clear_search_cache();
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:410:          `BM25 repair failed after reconsolidation merge for memory ${newId}: ${repairResult.error}`;
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:657: * @param options - Callbacks for similarity search and storage
.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:803:    console.warn('[reconsolidation] Immediate BM25 repair failed:', message);
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/lexical.ts:14:  find: ['search', 'locate'],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/lexical.ts:19:  search: ['find', 'locate', 'semantic'],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/lexical.ts:30:  'mcp-coco-index': ['semantic search', 'vector search', 'grep not enough', 'find code', 'where logic'],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/lexical.ts:31:  'sk-deep-research': ['deep research', 'research loop', 'overnight research', 'delta record', 'state log', 'lineage'],
.opencode/skills/system-spec-kit/mcp_server/lib/extraction/entity-extractor.ts:8:import { normalizeEntityName, computeEdgeDensity } from '../search/entity-linker.js';
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/002-pre-computed-hits-routing.md:28:- Prompt: `As a manual-testing orchestrator, run skill advisor twice for the same deployment query: first without semantic hits, then with pre-computed CocoIndex hits against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify sk-git appears in the semantic-hits run, its confidence is higher than in the baseline run, and the boosted reason references semantic input. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/002-pre-computed-hits-routing.md:39:| ADV-002 | Pre-computed hits routing | Verify `--semantic-hits` with JSON array boosts confidence for the referenced skill | `As a manual-testing orchestrator, run skill advisor twice for the same deployment query: first without semantic hits, then with pre-computed CocoIndex hits against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify sk-git appears in the semantic-hits run, its confidence is higher than in the baseline run, and the boosted reason references semantic input. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: python3 .opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py "deploy to production" --show-rejections` -> 2. Capture baseline JSON output and `sk-git` confidence if present -> 3. `bash: python3 .opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py "deploy to production" --semantic-hits '[{"path":".opencode/skills/sk-git/SKILL.md","score":0.92}]' --show-rejections` -> 4. Capture semantic-hits JSON output and compare the `sk-git` confidence against the baseline run | Both JSON outputs are valid; `sk-git` appears in the semantic-hits run; its confidence is higher than in the baseline run; boosted `reason` references semantic input | Baseline and semantic-hits JSON outputs with the `sk-git` entries highlighted | PASS if `sk-git` appears in the semantic-hits run with confidence higher than the baseline run; PARTIAL if `sk-git` appears but confidence is unchanged; FAIL if command errors or `sk-git` is absent from the semantic-hits run | Verify `--semantic-hits` JSON is valid (must be array of objects with `path` and `score`); check skill_advisor.py `SEMANTIC_BOOST_MULTIPLIER` config; confirm the same query string is used in both runs |
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:6:// PURPOSE: Route search/context results through one of four named
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:11://   research — results[] + evidenceDigest + followUps[]
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:24:import { resolveEffectiveScore, type PipelineRow } from '../search/pipeline/types.js';
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:29:export type ResponseProfile = 'quick' | 'research' | 'resume' | 'debug';
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:31:/** Generic search result entry as it arrives in the response data. */
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:85:/** Output of the `research` profile formatter. */
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:86:export interface ResearchProfile {
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:117:  | { profile: 'research'; data: ResearchProfile }
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:123:import { isResponseProfileEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:213:  // Suggest deeper search if top result has low score
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:230:    followUps.push(`Use memory_context with specFolder "${uniqueFolders[0]}" for full context`);
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:344: * Format results as the `research` profile.
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:348:function formatResearch(input: ProfileFormatterInput): ResearchProfile {
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:403: * Apply a named presentation profile to search results.
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:409: * @param profile       - Profile name ('quick' | 'research' | 'resume' | 'debug')
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:428:    case 'research':
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:429:      return { profile: 'research', data: formatResearch(safeInput) };
.opencode/skills/system-spec-kit/mcp_server/lib/response/profile-formatters.ts:511:  formatResearch,
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:2:title: "MCP-007 -- No-refresh search"
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:3:description: "This scenario validates No-refresh search for `MCP-007`. It focuses on Verify `refresh_index: false` skips reindexing and still returns results."
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:6:# MCP-007 -- No-refresh search
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:10:This scenario validates No-refresh search for `MCP-007`. It focuses on Verify `refresh_index: false` skips reindexing and still returns results.
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:20:- Prompt: `As a manual-testing orchestrator, search CocoIndex for "test" without triggering a reindex against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results array is non-empty; response time is noticeably faster than a refreshing search (no index wait notice). Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:21:- Expected signals: Results array is non-empty; response time is noticeably faster than a refreshing search (no index wait notice)
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:31:| MCP-007 | No-refresh search | Verify `refresh_index: false` skips reindexing and still returns results | `As a manual-testing orchestrator, search CocoIndex for "test" without triggering a reindex against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Results array is non-empty; response time is noticeably faster than a refreshing search (no index wait notice). Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "test utilities", "refresh_index": false })` -> 2. Verify results are returned AND no reindex was triggered | Results array is non-empty; response time is noticeably faster than a refreshing search (no index wait notice) | MCP output with timing noted; absence of `IndexWaitingNotice` in output | PASS if results returned without reindex delay; PARTIAL if results returned but unclear whether reindex was skipped; FAIL if no results or explicit reindex triggered | Compare timing with `refresh_index: true`; check daemon logs at `~/.cocoindex_code/daemon.log` for index activity |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md:48:- Feature file path: `02--mcp-search-tool/007-no-refresh-search.md`
.opencode/skills/system-spec-kit/mcp_server/hooks/gemini/compact-inject.ts:85:    'Context was compressed and auto-recovered. For full session state, call `memory_context({ mode: "resume", profile: "resume" })`.',
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:7:import { clearDegreeCacheForDb } from '../search/graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:11:import { isTemporalEdgesEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:162: * value in cache keys (e.g. memory_search when `enableCausalBoost=true`) so
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:166: * R-007-12 — targeted memory_search cache invalidation.
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:184:  // includes it (e.g. memory_search when enableCausalBoost=true) becomes
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:855: * Also: checklist SUPPORTS spec, decision-record SUPPORTS plan, research SUPPORTS spec
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:890:  if (ids.research && ids.spec) {
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:891:    edges.push({ sourceId: String(ids.research), targetId: String(ids.spec), relation: RELATION_TYPES.SUPPORTS, strength: 0.7, evidence: 'Spec 126: research supports spec' });
.opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:1085:  // R-007-12: Generation counter for memory_search cache invalidation
.opencode/skills/system-spec-kit/mcp_server/lib/response/README.md:35:| `profile-formatters.ts` | Profile reducers for `quick`, `research`, `resume`, and `debug` response shapes |
.opencode/skills/system-spec-kit/mcp_server/lib/response/README.md:43:- `profile-formatters.ts` exports `applyResponseProfile()` and `applyProfileToEnvelope()` plus the public profile types for `quick`, `research`, `resume`, and `debug`.
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/006-result-limit.md:20:- Prompt: `As a manual-testing orchestrator, compare CocoIndex search with 1 result vs 10 results against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 2: exactly 1 result; Step 4: result count between 1 and 10 (inclusive); Step 4 count >= Step 2 count. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/006-result-limit.md:31:| MCP-006 | Result limit | Verify `limit` controls output count | `As a manual-testing orchestrator, compare CocoIndex search with 1 result vs 10 results against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 2: exactly 1 result; Step 4: result count between 1 and 10 (inclusive); Step 4 count >= Step 2 count. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "error handling", "limit": 1 })` -> 2. Count results (expect exactly 1) -> 3. `mcp__cocoindex_code__search({ "query": "error handling", "limit": 10 })` -> 4. Count results (expect up to 10) | Step 2: exactly 1 result; Step 4: result count between 1 and 10 (inclusive); Step 4 count >= Step 2 count | Side-by-side result counts from both calls | PASS if step 2 returns exactly 1 AND step 4 returns more than 1 (up to 10); FAIL if `limit` is ignored | Verify `limit` parameter type is integer; check default (5) if parameter omitted |
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/006-result-limit.md:48:- Feature file path: `02--mcp-search-tool/006-result-limit.md`
.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:42:    toolPattern: /^(read|memory_context|memory_search|memory_list)$/i,
.opencode/skills/system-spec-kit/mcp_server/lib/extraction/extraction-adapter.ts:49:    toolPattern: /^(grep|memory_search)$/i,
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:14:  'research.md',
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:25:  '/research/iterations/',
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:34:  '/research/iterations/',
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:43:  '/research/iterations/',
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:82:export function isCanonicalResearchDocumentPath(filePath: string | null | undefined): boolean {
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:84:  return normalizedPath.endsWith('/research/research.md') || normalizedPath === 'research/research.md';
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:87:export function isLegacyOrCanonicalResearchDocumentPath(filePath: string | null | undefined): boolean {
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:89:  return normalizedPath.endsWith('/research.md')
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:90:    || normalizedPath === 'research.md'
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:91:    || isCanonicalResearchDocumentPath(normalizedPath);
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:134:  if (normalizedBasename === 'research.md') {
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:135:    if (!isLegacyOrCanonicalResearchDocumentPath(normalizedPath)) {
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:139:    if (parent === 'research') {
.opencode/skills/system-spec-kit/mcp_server/lib/config/spec-doc-paths.ts:187:  if (basename === 'research.md' && parent === 'research') {
.opencode/skills/system-spec-kit/mcp_server/handlers/save/post-insert.ts:15:} from '../../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/post-insert.ts:21:import { generateAndStoreSummary } from '../../lib/search/memory-summaries.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/post-insert.ts:22:import { runEntityLinkingForMemory } from '../../lib/search/entity-linker.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/post-insert.ts:23:import { onIndex, isGraphRefreshEnabled, type OnIndexSkipReason } from '../../lib/search/graph-lifecycle.js';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:14:import * as vectorIndexStore from '../lib/search/vector-index-store';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:76:    it('T517-2: handle_memory_match_triggers alias exported', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts:77:      expect(typeof handler.handle_memory_match_triggers).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:38:  /** Boosted confidence for `sk-deep-research` when the prompt carries
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:39:   * deep-research-cycle intent and `liveNormalized` clears the floor. */
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:40:  readonly deepResearchCycleSkillConfidence: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:41:  /** `liveNormalized` floor that the deep-research-cycle short-circuit
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:43:  readonly deepResearchCycleLiveNormalizedFloor: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:107:  // semantic search intent
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:108:  readonly semanticSearchCocoIndexBonus: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:109:  readonly semanticSearchDeepResearchPenalty: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:113:  // deep-research intent (text-only)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:114:  readonly deepResearchSkDeepResearchBonus: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:115:  readonly deepResearchOtherSkillsPenalty: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:116:  // deep-research-cycle phrase intent
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:117:  readonly deepResearchCycleSkDeepResearchBonus: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:118:  readonly deepResearchCycleOtherSkillsPenalty: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:126:  readonly slashCommandDeepResearchBonus: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:130:  readonly phaseFolderDeepResearchPenalty: number;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:148:    deepResearchCycleSkillConfidence: 0.84,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:149:    deepResearchCycleLiveNormalizedFloor: 0.12,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:175:    semanticSearchCocoIndexBonus: 0.5,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:176:    semanticSearchDeepResearchPenalty: -0.2,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:179:    deepResearchSkDeepResearchBonus: 0.35,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:180:    deepResearchOtherSkillsPenalty: -0.18,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:181:    deepResearchCycleSkDeepResearchBonus: 0.45,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:182:    deepResearchCycleOtherSkillsPenalty: -0.18,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:187:    slashCommandDeepResearchBonus: 0.45,
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/scoring-constants.ts:190:    phaseFolderDeepResearchPenalty: -0.25,
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:47:  name: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:48:  description: '[L1:Orchestration] Unified entry point for context retrieval with intent-aware routing. START HERE for most context-retrieval operations across indexed spec docs and constitutional rules. For session recovery, use mode: \'resume\' with profile: \'resume\'. Automatically detects task intent (add_feature, fix_bug, refactor, security_audit, understand, find_spec, find_decision) and routes to optimal retrieval strategy. Modes: auto (default), quick (trigger-based), deep (comprehensive), focused (intent-optimized), resume (session recovery). Token Budget: 3500. For code search by concept/intent, prefer mcp__cocoindex_code__search (CocoIndex). For structural code queries (callers, imports), prefer code_graph_query.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:49:  inputSchema: { type: 'object', additionalProperties: false, properties: { input: { type: 'string', minLength: 1, description: 'The query, prompt, or context description (required)' }, mode: { type: 'string', enum: ['auto', 'quick', 'deep', 'focused', 'resume'], default: 'auto', description: 'Context retrieval mode: auto (detect intent), quick (fast triggers), deep (comprehensive search), focused (intent-optimized), resume (session recovery)' }, intent: { type: 'string', enum: ['add_feature', 'fix_bug', 'refactor', 'security_audit', 'understand', 'find_spec', 'find_decision'], description: 'Explicit task intent. If not provided and mode=auto, intent is auto-detected from input.' }, specFolder: { type: 'string', description: 'Limit context to specific spec folder' }, tenantId: { type: 'string', description: 'Tenant boundary for governed retrieval when memory_context routes to memory_search.' }, userId: { type: 'string', description: 'User boundary for governed retrieval when memory_context routes to memory_search.' }, agentId: { type: 'string', description: 'Agent boundary for governed retrieval when memory_context routes to memory_search.' }, limit: { type: 'number', minimum: 1, maximum: 100, description: 'Maximum results (mode-specific defaults apply)' }, sessionId: { type: 'string', description: 'Optional server-issued session identifier for working-memory continuity. When provided, it must match an existing server-managed session or the call is rejected. Omit it to let the server generate a new session for this request.' }, enableDedup: { type: 'boolean', default: true, description: 'Enable session deduplication' }, includeContent: { type: 'boolean', default: false, description: 'Include full file content in results' }, includeTrace: { type: 'boolean', default: false, description: 'Include provenance-rich trace data (scores, source, trace) in results when underlying memory_search is called' }, tokenUsage: { type: 'number', minimum: 0.0, maximum: 1.0, description: "Optional caller token usage ratio (0.0-1.0)" }, anchors: { type: 'array', items: { type: 'string' }, description: 'Filter content to specific anchors (e.g., ["state", "next-steps"] for resume mode)' }, profile: { type: 'string', enum: ['quick', 'research', 'resume', 'debug'], description: 'Optional response profile formatter. Returns a reduced or mode-aware response shape when profile formatting is enabled.' } }, required: ['input'] },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:54:  name: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:55:  description: '[L2:Core] Search indexed spec-doc continuity semantically using vector similarity. Returns ranked results with similarity scores. Constitutional tier rules are ALWAYS included at the top of results (~2000 tokens max), regardless of query. Requires query (string), concepts (array of 2-5 strings), or cursor (string) for continuation pagination. Supports intent-aware retrieval (REQ-006) with task-specific weight adjustments. When implicit feedback logging is enabled, searches also emit shadow-only feedback signals such as search_shown and, for includeContent runs, result_cited. Token Budget: 3500. For code search by concept/intent, prefer mcp__cocoindex_code__search (CocoIndex). For structural code queries (callers, imports), prefer code_graph_query.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:66:      query: { type: 'string', minLength: 2, maxLength: 1000, description: 'Natural language search query' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:72:        description: 'Multiple concepts for AND search (requires 2-5 concepts). Results must match ALL concepts.'
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:74:      specFolder: { type: 'string', description: 'Limit search to a specific spec folder (e.g., "011-spec-kit-memory-upgrade")' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:89:      contextType: { type: 'string', description: 'Filter by context type (decision, implementation, research, etc.)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:108:        description: 'Include full file content in results. When true, each result includes a "content" field with the spec-doc file contents. This embeds load logic directly in search, eliminating the need for separate load calls. When implicit feedback logging is enabled, includeContent searches also emit shadow-only result_cited events for returned spec-doc records.'
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:117:        enum: ['quick', 'research', 'resume', 'debug'],
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:135:        description: 'Skip the tool cache and force a fresh search. Useful when underlying data has changed since last cached result.'
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:177:        description: 'Include archived spec-doc records in search results. Default: false (archived excluded).'
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:194:// E3: Simplified search — 3 params, sensible defaults, delegates to memory_search
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:196:  name: 'memory_quick_search',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:197:  description: '[L2:Core] Simplified search — query + optional limit + optional spec folder. Delegates to memory_search with sensible defaults (intent auto-detect ON, dedup ON, content included, limit 10). Use this when you want fast search without configuring 31 parameters.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:202:      query: { type: 'string', minLength: 2, maxLength: 1000, description: 'Natural language search query' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:214:  name: 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:223:  inputSchema: { type: 'object', additionalProperties: false, properties: { filePath: { type: 'string', minLength: 1, description: 'Absolute path to a spec document under specs/**/ or .opencode/specs/**/ (spec.md, plan.md, tasks.md, checklist.md, decision-record.md, implementation-summary.md, handover.md, research.md, resource-map.md, description.json, graph-metadata.json) or a constitutional memory under .opencode/skills/*/constitutional/' }, force: { type: 'boolean', default: false, description: 'Force re-index even if content hash unchanged' }, dryRun: { type: 'boolean', default: false, description: 'Validate only without saving. Returns validation results including anchor format, duplicate check, and token budget estimation (CHK-160)' }, skipPreflight: { type: 'boolean', default: false, description: 'Skip pre-flight validation checks (not recommended)' }, asyncEmbedding: { type: 'boolean', default: false, description: 'When true, embedding generation is deferred for non-blocking saves. The spec-doc record is immediately saved with pending status and an async background attempt is triggered. Default false preserves synchronous embedding behavior.' }, routeAs: { type: 'string', enum: ['narrative_progress', 'narrative_delivery', 'decision', 'handover_state', 'research_finding', 'task_update', 'metadata_only', 'drop'], description: 'Optional routing override hint for canonical continuity saves.' }, mergeModeHint: { type: 'string', enum: ['append-as-paragraph', 'insert-new-adr', 'append-table-row', 'update-in-place', 'append-section'], description: 'Optional merge-mode hint for routed canonical continuity saves.' }, tenantId: { type: 'string', description: 'Tenant boundary for governed ingest.' }, userId: { type: 'string', description: 'User boundary for governed ingest.' }, agentId: { type: 'string', description: 'Agent boundary for governed ingest.' }, sessionId: { type: 'string', description: 'Session boundary for governed ingest.' }, provenanceSource: { type: 'string', description: 'Required provenance source when governed ingest validation applies.' }, provenanceActor: { type: 'string', description: 'Required provenance actor when governed ingest validation applies.' }, governedAt: { type: 'string', description: 'ISO timestamp for governed ingest. Defaults to now when omitted.' }, retentionPolicy: { type: 'string', enum: ['keep', 'ephemeral'], description: 'Retention class applied to the saved spec-doc record.' }, deleteAfter: { type: 'string', description: 'Optional ISO timestamp after which retention sweep may delete the spec-doc record.' } }, required: ['filePath'] },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:266:        description: 'When true in full mode, attempts best-effort repair actions for detected health issues (e.g., FTS rebuild).'
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:311:      resultRank: { type: 'number', minimum: 1, description: 'Optional rank position (1-based) of the selected spec-doc record in search results' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:313:      searchMode: { type: 'string', description: 'Optional search mode context (search/context/trigger)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:496:  inputSchema: { type: 'object', additionalProperties: false, properties: { specFolder: { type: 'string', description: 'Limit scan to specific spec folder (e.g., "005-memory")' }, force: { type: 'boolean', default: false, description: 'Force re-index all files (ignore content hash)' }, includeConstitutional: { type: 'boolean', default: true, description: 'Whether to scan .opencode/skills/*/constitutional/ directories' }, includeSpecDocs: { type: 'boolean', default: true, description: 'Whether to scan .opencode/specs/ directories for spec folder documents (spec.md, plan.md, tasks.md, checklist.md, decision-record.md, implementation-summary.md, research/research.md, handover.md, resource-map.md). Iteration artifacts under research/iterations/ and review/iterations/ are excluded from spec-doc indexing. Set SPECKIT_INDEX_SPEC_DOCS=false env var to disable globally.' }, incremental: { type: 'boolean', default: true, description: 'Enable incremental indexing. When true (default), skips files whose mtime and content hash are unchanged since last index. Set to false to re-evaluate all files regardless of change detection.' } }, required: [] },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:573:  name: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:599:  name: 'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:600:  description: '[L6:Analysis] Get LLM-oriented compact graph neighborhoods. Accepts CocoIndex search results as seeds — use CocoIndex (mcp__cocoindex_code__search) for semantic search first, then pass results here for structural expansion. Supports manual seeds (provider: manual) and graph seeds (provider: graph). Modes: neighborhood (1-hop calls+imports), outline (file symbols), impact (reverse callers). When readiness requires a full scan, returns an explicit blocked payload with requiredAction `code_graph_scan`, readiness metadata, and lastPersistedAt instead of degraded graph answers. Successful responses include metadata.partialOutput for deadline/budget truncation details (reasons, omittedSections, omittedAnchors, truncatedText). Token Budget: 1200.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:618:            file: { type: 'string', description: 'CocoIndex file path (provider: cocoindex)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:619:            range: { type: 'object', properties: { start: { type: 'number' }, end: { type: 'number' } }, description: 'CocoIndex line range' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:620:            score: { type: 'number', description: 'CocoIndex relevance score' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:621:            snippet: { type: 'string', description: 'CocoIndex snippet text preserved with the seed' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:628:        description: 'Seeds from CocoIndex, manual input, or graph lookups',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:631:      profile: { type: 'string', enum: ['quick', 'research', 'debug'], description: 'Output density profile' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:718:  description: '[L7:Maintenance] Check CocoIndex availability. Returns available, binaryPath, indexExists, indexSize, and recommendation.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:724:  description: '[L7:Maintenance] Trigger CocoIndex incremental (or full) re-indexing of the workspace.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:736:  description: '[L7:Maintenance] Submit quality feedback on CocoIndex search results to improve future searches.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:740:      query: { type: 'string', description: 'The search query that was executed' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:759:  description: '[L1:Orchestration] Resume session with combined memory, code graph, and CocoIndex status in a single call. Use when you want the detailed merged resume payload directly. For the canonical first-call recovery path on session start or after /clear, prefer session_bootstrap. Use minimal: true to skip the heavy memory context call and return code graph, CocoIndex, structural context, hints, and session-quality metadata without the full memory payload.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:766:      minimal: { type: 'boolean', description: 'When true, skip the heavy memory context call and return code-graph, CocoIndex, structural-context, hints, and session-quality fields without the full memory payload' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:805:      loopType: { type: 'string', enum: ['research', 'review'], description: 'Loop type: research or review (required)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:813:            kind: { type: 'string', description: 'Node kind. Research: QUESTION, FINDING, CLAIM, SOURCE. Review: DIMENSION, FILE, FINDING, EVIDENCE, REMEDIATION' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:831:            relation: { type: 'string', description: 'Edge relation type. Research: ANSWERS, SUPPORTS, CONTRADICTS, SUPERSEDES, DERIVED_FROM, COVERS, CITES. Review: COVERS, EVIDENCE_FOR, CONTRADICTS, RESOLVES, CONFIRMS, ESCALATES, IN_DIMENSION, IN_FILE' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:851:      loopType: { type: 'string', enum: ['research', 'review'], description: 'Loop type (required)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:869:      loopType: { type: 'string', enum: ['research', 'review'], description: 'Loop type (required)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:878:  description: '[L9:CoverageGraph] Composite convergence assessment for deep-loop coverage graph. Returns a typed decision (CONTINUE, STOP_ALLOWED, STOP_BLOCKED), signal values, blockers with severity levels, and a typed trace explaining each signal threshold evaluation. For research: evaluates questionCoverage, claimVerificationRate, contradictionDensity, plus blocking guards sourceDiversity and evidenceDepth. For review: evaluates dimensionCoverage, findingStability, p0ResolutionRate, evidenceDensity, hotspotSaturation. Extends Phase 001 stop logic without replacing newInfoRatio.',
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:883:      loopType: { type: 'string', enum: ['research', 'review'], description: 'Loop type (required)' },
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:954:  // L8: CocoIndex
.opencode/skills/system-spec-kit/mcp_server/lib/response/envelope.ts:150:    'Try broadening your search query',
.opencode/skills/system-spec-kit/mcp_server/lib/extraction/README.md:240:| `lib/search/entity-linker.ts` | Cross-document entity linking (S5), consumes entities extracted by R10 |
.opencode/skills/system-spec-kit/mcp_server/tests/hook-session-stop.vitest.ts:185:      lastSpecFolder: 'specs/system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research',
.opencode/skills/system-spec-kit/mcp_server/tests/hook-session-stop.vitest.ts:320:      lastSpecFolder: 'specs/system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research',
.opencode/skills/system-spec-kit/mcp_server/tests/hook-session-stop.vitest.ts:391:      'specs/system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research/tasks.md',
.opencode/skills/system-spec-kit/mcp_server/tests/hook-session-stop.vitest.ts:444:        'specs/system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research',
.opencode/skills/system-spec-kit/mcp_server/tests/hook-session-stop.vitest.ts:661:      lastSpecFolder: 'specs/system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research',
.opencode/skills/system-spec-kit/mcp_server/handlers/save/response-builder.ts:398:    result.message = 'Memory saved with deferred indexing - searchable via BM25/FTS5';
.opencode/skills/system-spec-kit/mcp_server/handlers/save/response-builder.ts:645:      response.message = `${response.message} (deferred indexing - searchable via BM25/FTS5)`;
.opencode/skills/system-spec-kit/mcp_server/handlers/save/response-builder.ts:667:    hints.push('Review anchor warnings for better searchability');
.opencode/skills/system-spec-kit/mcp_server/handlers/save/response-builder.ts:691:      hints.push('Post-insert enrichment was deferred; runEnrichmentBackfill when immediate graph/search freshness matters');
.opencode/skills/system-spec-kit/mcp_server/tests/startup-brief.vitest.ts:50:  isCocoIndexAvailable: vi.fn(() => false),
.opencode/skills/system-spec-kit/mcp_server/tests/startup-brief.vitest.ts:77:    expect(brief.startupSurface).toContain('- CocoIndex: missing');
.opencode/skills/system-spec-kit/mcp_server/tests/startup-brief.vitest.ts:134:    vi.mocked(cocoIndexPath.isCocoIndexAvailable).mockReturnValueOnce(true);
.opencode/skills/system-spec-kit/mcp_server/tests/startup-brief.vitest.ts:137:    expect(brief.startupSurface).toContain('- CocoIndex: available');
.opencode/skills/system-spec-kit/mcp_server/tests/startup-brief.vitest.ts:143:    expect(brief.graphOutline).toContain('CocoIndex');
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/002-full-index-build.md:28:- Prompt: `As a manual-testing orchestrator, build the full semantic index for this project against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Output contains numeric file and chunk counts (for example "Files:" and "Chunks:" or similar metric lines). Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/002-full-index-build.md:39:| CCC-002 | Full index build | Verify `ccc index` reports file count and chunk count | `As a manual-testing orchestrator, build the full semantic index for this project against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Output contains numeric file and chunk counts (for example "Files:" and "Chunks:" or similar metric lines). Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: ccc index` -> 2. Capture output containing file count and chunk count | Output contains numeric file and chunk counts (for example `Files:` and `Chunks:` or similar metric lines) | Index build transcript with file/chunk counts highlighted | PASS if output contains non-zero file count AND non-zero chunk count; FAIL if either count is zero or missing | Check `.cocoindex_code/settings.yml` include_patterns; verify project has indexable source files; check daemon connectivity |
.opencode/skills/system-spec-kit/mcp_server/tests/confidence-truncation.vitest.ts:19:} from '../lib/search/confidence-truncation';
.opencode/skills/system-spec-kit/mcp_server/tests/confidence-truncation.vitest.ts:201:    // Since minResults=3 and we start search at index 2, gap[0] is skipped
.opencode/skills/system-spec-kit/mcp_server/tests/confidence-truncation.vitest.ts:208:    // Start search at i=2 (minResults-1 = 2):
.opencode/skills/system-spec-kit/mcp_server/tests/confidence-truncation.vitest.ts:213:    // With the actual numbers the large gap at 0 is not searched; no truncation
.opencode/skills/system-spec-kit/mcp_server/tests/confidence-truncation.vitest.ts:218:    // With minResults=2 we start searching at gap[1]
.opencode/skills/system-spec-kit/mcp_server/lib/extraction/ontology-hooks.ts:12:import { isOntologyHooksEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:9:// CRITICAL: This column MUST NOT be added to the FTS5 index.
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:39:/** Column name for learned triggers (NOT in FTS5 index) */
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:54: * the memory_fts FTS5 virtual table. The FTS5 index columns are:
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:57: * isolated from the organic search index.
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:90:// 4. FTS5 ISOLATION VERIFICATION
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:95: * FTS5 index (memory_fts). This is a safety check that should be run
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:98: * The FTS5 virtual table memory_fts should only contain:
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:101: * If learned_triggers appears in FTS5, it means user-generated feedback
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:102: * has polluted the organic search index -- a data integrity violation.
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:105: * @returns true if isolation is verified (learned_triggers NOT in FTS5)
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:106: * @throws Error if learned_triggers IS found in FTS5 (critical violation)
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:110:    // Check if FTS5 table exists
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:116:      // FTS5 table does not exist; isolation trivially holds
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:122:    // Check that learned_triggers does NOT appear in the FTS5 CREATE statement
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:125:        'CRITICAL: learned_triggers found in FTS5 index (memory_fts). ' +
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:127:        'ONLY exist in the memory_index.learned_triggers column, never in FTS5.'
.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts:137:    console.error(`[learned-triggers-schema] FTS5 isolation check failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:44:const DEEP_RESEARCH_CYCLE = /\b(automated research cycle|looped investigation|continue iteration|resume iteration|overnight run|overnight research run|packet-local iteration|delta record|canonical jsonl|same lineage)\b/;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:104:  hasDeepResearchCycleIntent: boolean;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:120:  if (args.hasDeepResearchCycleIntent
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:121:    && args.skillId === 'sk-deep-research'
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:122:    && args.liveNormalized >= C.deepResearchCycleLiveNormalizedFloor) {
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:123:    return C.deepResearchCycleSkillConfidence;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:201:  if (skillId === 'sk-deep-research' && /\b(deep-loop prompts|ordinary file-write prompts|research cycle|same corpus)\b/.test(promptLower)) {
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:218:  if (/\bsemantic (code )?search\b/.test(promptLower)) {
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:219:    const activeDeepResearch = /\/spec_kit:deep-research|\b(resume|continue|run|launch|start|iteration|convergence)\b.*\bdeep[- ]research\b/.test(promptLower);
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:220:    if (recommendation.skill === 'mcp-coco-index') return R.semanticSearchCocoIndexBonus;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:221:    if (!activeDeepResearch && recommendation.skill === 'sk-deep-research') return R.semanticSearchDeepResearchPenalty;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:227:  if (/\bdeep[- ]research\b/.test(promptLower)) {
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:228:    if (recommendation.skill === 'sk-deep-research') return R.deepResearchSkDeepResearchBonus;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:229:    if (recommendation.skill === 'system-spec-kit' || recommendation.skill === 'sk-code-review') return R.deepResearchOtherSkillsPenalty;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:232:    if (recommendation.skill === 'sk-deep-research') return R.deepResearchCycleSkDeepResearchBonus;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:233:    if (recommendation.skill === 'system-spec-kit' || recommendation.skill === 'sk-code-review' || recommendation.skill === 'sk-code-opencode') return R.deepResearchCycleOtherSkillsPenalty;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:243:  if (promptLower.includes('/spec_kit:deep-research') && recommendation.skill === 'sk-deep-research') return R.slashCommandDeepResearchBonus;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:247:    if (recommendation.skill === 'sk-deep-research') return R.phaseFolderDeepResearchPenalty;
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:270:  const hasDeepResearchCycleIntent = DEEP_RESEARCH_CYCLE.test(promptLower);
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts:310:      hasDeepResearchCycleIntent,
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md:2:title: "CCC-004 -- CLI search with filters"
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md:3:description: "This scenario validates CLI search with filters for `CCC-004`. It focuses on Verify `--lang` (repeatable) and `--limit` filters work."
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md:6:# CCC-004 -- CLI search with filters
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md:10:This scenario validates CLI search with filters for `CCC-004`. It focuses on Verify `--lang` (repeatable) and `--limit` filters work.
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md:20:- Prompt: `As a manual-testing orchestrator, search for "function" filtered to Python and TypeScript with limit 3 against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: returns results; Step 2: all file extensions are .py, .ts, or .tsx; Step 3: result count <= 3. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md:31:| CCC-004 | CLI search with filters | Verify `--lang` (repeatable) and `--limit` filters work | `As a manual-testing orchestrator, search for "function" filtered to Python and TypeScript with limit 3 against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: returns results; Step 2: all file extensions are .py, .ts, or .tsx; Step 3: result count <= 3. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: ccc search "function" --lang python --lang typescript --limit 3` -> 2. Verify all returned file paths end in `.py` or `.ts`/`.tsx` -> 3. Verify result count is at most 3 | Step 1: returns results; Step 2: all file extensions are `.py`, `.ts`, or `.tsx`; Step 3: result count <= 3 | Search output with file paths and count | PASS if all results match language filter AND count <= 3; PARTIAL if count correct but one result has wrong extension; FAIL if filter is ignored | Check `--lang` values against supported language code values in tool_reference.md; verify index contains Python/TypeScript files |
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md:48:- Feature file path: `01--core-cli-commands/004-cli-search-with-filters.md`
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:17:    vi.doUnmock('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:18:    vi.doUnmock('../lib/search/search-flags.js');
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:34:    vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:35:      const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:45:    vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:46:      const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:93:    vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:94:      const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:104:    vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:105:      const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:158:    vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:159:      const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:169:    vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/retry-budget-telemetry.vitest.ts:170:      const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-extended.vitest.ts:19:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-extended.vitest.ts:777:        contextType: 'research',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-extended.vitest.ts:784:      expect(result.contextType).toBe('research');
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:72:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:75:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:97:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:137:  - Handler-level mutation/search/reporting paths that surface recovery hints
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:141:- Purpose: Owns evaluation, baselines, shadow measurements, quality proxies, and reporting artifacts for retrieval quality. It is the measurement and experimentation layer for search behavior.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:150:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:176:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:178:  - `lib/search/search-flags.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:188:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:190:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:200:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:211:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:225:- Purpose: Reserved for future scheduled or batch-style memory-management algorithms that are not part of the live search path. The deprecated PageRank helper was removed after the dead-code audit confirmed it was never wired.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:247:  - `content-normalizer.ts` — normalization helpers for file content and search/index inputs.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:252:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:260:  - `embeddings.ts` — shared-package-backed embeddings surface used by index/search code.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:265:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:278:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:293:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:299:### `search/`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:301:- Purpose: Owns the retrieval engine: candidate generation, vector/lexical channels, fusion, reranking, query intelligence, graph-aware retrieval, and schema/index helpers needed by the search path. This is the highest-churn and broadest domain module in `lib/`.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:303:  - `hybrid-search.ts` — main hybrid retrieval entry point across search channels.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:306:  - `vector-index-schema.ts` — schema creation and schema-safety helpers for search storage.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:310:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:323:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:337:- Purpose: Owns persistence behavior outside the search algorithm itself: checkpoints, history, access tracking, lineage state, transactions, consolidation, reconsolidation, and index refresh flows. This is the long-lived state management layer for the indexed-continuity store.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:350:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:363:  - `handlers/memory-search.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:378:  - `lib/search/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:448:| `search` | `01--retrieval`, `03--discovery`, `06--analysis`, `10--graph-signal-activation`, `11--scoring-and-calibration`, `12--query-intelligence`, `14--pipeline-architecture`, `15--retrieval-enhancements`, `19--feature-flag-reference` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:460:| `01--retrieval` | `cache`, `parsing`, `providers`, `search` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:462:| `03--discovery` | `search` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:465:| `06--analysis` | `graph`, `search` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:469:| `10--graph-signal-activation` | `graph`, `manage`, `scoring`, `search`, `storage` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:470:| `11--scoring-and-calibration` | `cognitive`, `config`, `feedback`, `learning`, `manage`, `scoring`, `search`, `telemetry` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:471:| `12--query-intelligence` | `parsing`, `search` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:473:| `14--pipeline-architecture` | `architecture`, `contracts`, `interfaces`, `response`, `search`, `spec` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:474:| `15--retrieval-enhancements` | `cache`, `chunking`, `cognitive`, `graph`, `providers`, `scoring`, `search`, `session` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:478:| `19--feature-flag-reference` | `cognitive`, `config`, `feedback`, `search` |
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:525:- They should not import domain modules such as `search`, `cognitive`, `storage`, or `scoring`.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:542:- `telemetry` should accept trace/metric payloads from `search`, `scoring`, or handlers, but not import retrieval logic from them.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:563:- `storage` should not depend on `search` ranking logic; `search` may depend on `storage`.
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:575:- `search`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:587:  - Must not import: `search`, `storage`, `scoring`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:590:  - Must not import: `search`, `storage`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:593:  - Must not import: `search`, `storage`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:596:  - Must not import: `search`, `storage`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:599:  - Must not import: `search` orchestration, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:602:  - Must not import: `search`, `storage`, `telemetry`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:603:- `search`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:609:  - Must not import: `search`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:612:  - Must not import: `search`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:614:  - May import: core, `search`, `scoring`, `telemetry`, `storage`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:617:  - May import: core, `search`, `scoring`, `storage`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:621:  - Must not import: `search`, `collab`, handlers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:624:  - Must not import: `search` directly except through neutral shared contracts/helpers
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:632:- lower-level modules importing `search` as a convenience helper
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:633:- `storage -> search`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:636:- `validation -> search`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:637:- `telemetry -> search`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:645:- `telemetry/retrieval-telemetry.ts -> search/session-transition.ts`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:646:- `validation/* -> search/*` and `chunking/*`
.opencode/skills/system-spec-kit/mcp_server/lib/MODULE_MAP.md:647:- `storage/* -> search/*`
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/text.ts:96:  const skillSurface = /\b(review|audit|deep[- ]research|deep[- ]review|semantic search|figma|clickup|chrome devtools|git worktree|prompt)\b/.test(promptLower);
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/projection.ts:50:    keywords: ['/spec_kit:plan', '/spec_kit:resume', '/spec_kit:deep-research', '/spec_kit:deep-review'],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/projection.ts:52:    intentSignals: ['/spec_kit:plan', '/spec_kit:resume', '/spec_kit:deep-research', '/spec_kit:deep-review'],
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:6:  { tool: 'memory_context', handler: 'handleMemoryContext', layer: 'L1' },
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:7:  { tool: 'memory_search', handler: 'handleMemorySearch', layer: 'L2' },
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:8:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers', layer: 'L2' },
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:33:  { camel: 'handleMemorySearch', snake: 'handle_memory_search' },
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:34:  { camel: 'handleMemoryMatchTriggers', snake: 'handle_memory_match_triggers' },
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-tool-dispatch.vitest.ts:56:  { camel: 'handleMemoryContext', snake: 'handle_memory_context' },
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/003-incremental-index.md:20:- Prompt: `As a manual-testing orchestrator, create a temp file, reindex, search for it, delete it, reindex again against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 3: search returns at least 1 result referencing ccc_test_incremental.py; Step 6: search returns 0 results for that file. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/003-incremental-index.md:21:- Expected signals: Step 3: search returns at least 1 result referencing `ccc_test_incremental.py`; Step 6: search returns 0 results for that file
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/003-incremental-index.md:31:| CCC-003 | Incremental index | Verify incremental indexing picks up new content and drops deleted content | `As a manual-testing orchestrator, create a temp file, reindex, search for it, delete it, reindex again against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 3: search returns at least 1 result referencing ccc_test_incremental.py; Step 6: search returns 0 results for that file. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: echo '# Temporary test: xyzzy_incremental_test_marker' > /tmp/ccc_test_incremental.py && cp /tmp/ccc_test_incremental.py ./ccc_test_incremental.py` -> 2. `bash: ccc index` -> 3. `bash: ccc search "xyzzy_incremental_test_marker" --limit 3` -> 4. `bash: rm ./ccc_test_incremental.py` -> 5. `bash: ccc index` -> 6. `bash: ccc search "xyzzy_incremental_test_marker" --limit 3` | Step 3: search returns at least 1 result referencing `ccc_test_incremental.py`; Step 6: search returns 0 results for that file | Transcript of all 6 steps; search output from steps 3 and 6 | PASS if step 3 finds the temp file AND step 6 does not; PARTIAL if step 3 finds it but step 6 still returns stale results; FAIL if step 3 does not find the temp file | Re-run `ccc index`; check if daemon cached stale data; verify `.gitignore` is not excluding the temp file |
.opencode/skills/system-spec-kit/mcp_server/lib/context/shared-payload.ts:209: * @see .opencode/specs/system-spec-kit/026-graph-and-context-optimization/009-hook-package/001-skill-advisor-hook-surface/001-initial-research/research/020-skill-advisor-hook-surface-pt-01/research.md
.opencode/skills/system-spec-kit/mcp_server/lib/storage/document-helpers.ts:29:        research: 0.6,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-delete.ts:10:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-delete.ts:21:import { clearDegreeCacheForDb } from '../lib/search/graph-search-fn.js';
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/005-index-reset-destructive.md:20:- Prompt: `As a manual-testing orchestrator, reset the CocoIndex Code index completely and rebuild against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: exits without error; Step 2: shows zero files or "not initialized"; Step 4: rebuilds with non-zero counts; Step 5: shows non-zero file and chunk counts. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/005-index-reset-destructive.md:31:| CCC-005 | Index reset **(DESTRUCTIVE)** | Verify `ccc reset --all` clears index; status shows empty; rebuild succeeds | `As a manual-testing orchestrator, reset the CocoIndex Code index completely and rebuild against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: exits without error; Step 2: shows zero files or "not initialized"; Step 4: rebuilds with non-zero counts; Step 5: shows non-zero file and chunk counts. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: ccc reset --all -f` -> 2. `bash: ccc status` (expect zero/empty counts) -> 3. `bash: ccc init` -> 4. `bash: ccc index` -> 5. `bash: ccc status` (expect non-zero counts) | Step 1: exits without error; Step 2: shows zero files or "not initialized"; Step 4: rebuilds with non-zero counts; Step 5: shows non-zero file and chunk counts | Full transcript of all 5 steps; before/after status output | PASS if reset clears index AND rebuild restores non-zero counts; FAIL if reset errors or rebuild produces zero counts | Check `ccc reset` flags; verify `-f` bypasses confirmation; check disk space for rebuild |
.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:109:Write-driven invalidation is used for memory and spec document changes so search and ranking do not serve stale `documentType`/`specLevel` context.
.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:182:const key = generateCacheKey('memory_search', { query: 'test' });
.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:185:set(key, searchResults, { toolName: 'memory_search', ttlMs: 30000 });
.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:197:  'memory_search',
.opencode/skills/system-spec-kit/mcp_server/lib/cache/README.md:211:// Automatically clears memory_search, memory_match_triggers, etc.
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/001-project-initialization.md:20:- Prompt: `As a manual-testing orchestrator, initialize a new CocoIndex Code project in the current directory against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 2: output contains "Initialized" or creates .cocoindex_code/; Step 3: file exists; Step 4: output contains "already" or exits without error; Step 5: succeeds without error; Step 6: file exists. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/001-project-initialization.md:31:| CCC-001 | Project initialization | Verify `ccc init` creates project config; second call reports already initialized; `--force` re-creates | `As a manual-testing orchestrator, initialize a new CocoIndex Code project in the current directory against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 2: output contains "Initialized" or creates .cocoindex_code/; Step 3: file exists; Step 4: output contains "already" or exits without error; Step 5: succeeds without error; Step 6: file exists. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: rm -rf .cocoindex_code/` -> 2. `bash: ccc init` -> 3. Verify `.cocoindex_code/settings.yml` exists: `bash: ls .cocoindex_code/settings.yml` -> 4. `bash: ccc init` (second call, expect "already initialized" or similar) -> 5. `bash: ccc init -f` (force re-create) -> 6. `bash: ls .cocoindex_code/settings.yml` | Step 2: output contains "Initialized" or creates `.cocoindex_code/`; Step 3: file exists; Step 4: output contains "already" or exits without error; Step 5: succeeds without error; Step 6: file exists | Terminal transcript of all 6 steps with timestamps | PASS if all 6 steps produce expected signals; FAIL if `settings.yml` missing after init or `--force` errors | Check `ccc` binary path; verify Python 3.11+; check write permissions on project root |
.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:312:    'memory_search',
.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:313:    'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/lib/cache/tool-cache.ts:314:    'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:11:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:12:import type { UpdateMemoryParams } from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:14:import * as bm25Index from '../lib/search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:144:  // Cache invalidation, BM25 re-index, ledger append) in a single transaction for atomicity.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:210:      // T2-6 — BM25 index stores title + trigger phrases; must re-index when either changes
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:211:      // So keyword search reflects the updated content.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:212:      // T-05: BM25 re-index failure now rolls back the transaction when the index is operational.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:213:      // Infrastructure failures (BM25 not available, DB missing prepare) are non-fatal warnings.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:229:          // Infrastructure failures mean the BM25 subsystem is unavailable or torn down —
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:240:            console.warn(`[memory-crud-update] BM25 infrastructure unavailable, skipping re-index [requestId=${requestId}]: ${bm25ErrMsg}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:242:            console.error(`[memory-crud-update] BM25 re-index failed, rolling back update [requestId=${requestId}]: ${bm25ErrMsg}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:243:            throw new Error(`BM25 re-index failed: ${bm25ErrMsg}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts:325:    hints.push('Embedding regenerated - search results may differ');
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:5:// Records implicit feedback signals from search/save interactions
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:12://   weak    — search_shown, same_topic_requery (passive exposure)
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:23: *   result_cited | follow_on_tool_use > query_reformulated > same_topic_requery > search_shown
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:26:  | 'search_shown'
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:83:  search_shown:         'weak',
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:119:                 'search_shown','result_cited','query_reformulated',
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:164: * Shadow-only: this function has NO effect on search ranking.
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:169: * never interrupt search or save operations.
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:203: * Record a batch of feedback events (e.g., all search_shown results from
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/feedback-ledger.ts:204: * a single search response).
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:8:// Embedding generation or BM25 indexing.  Raw markdown contains
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:19:// → normalizeContentForBM25(content_text)
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:99: *   | Grep | search  | active |
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:103: *   Grep search active
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:235: * Normalize markdown content for use in BM25 keyword indexing.
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:237: * BM25 benefits from the same structural noise removal as the
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:240: * (function names, class names, CLI flags) remain searchable.
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:255:export function normalizeContentForBM25(content: string): string {
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:256:  // The BM25 pipeline currently delegates to the same normalization
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/content-normalizer.ts:259:  // A separate entry point exists so BM25-specific adjustments
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/tier-classifier.ts:17: * fallbacks, search-enriched properties, etc.).
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:12:import * as crossEncoder from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:15:import type { RerankDocument } from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:26:    query: 'how does the hybrid search pipeline work',
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:70:    { id: 904, content: 'Hybrid search fallback notes and unrelated ranking guidance. '.repeat(2) },
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:71:    { id: 102, content: 'Hybrid search uses reciprocal rank fusion to combine sparse and dense scores. '.repeat(2) },
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:72:    { id: 101, content: 'Hybrid search pipeline runs lexical retrieval, vector retrieval, and reranking in sequence. '.repeat(2) },
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:85:    { id: 903, content: 'Background note about search result explainability output. '.repeat(2) },
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts:94:    { id: 402, content: 'Save-context indexing turns new memories into searchable retrieval candidates. '.repeat(2) },
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:5:// code graph status, and CocoIndex availability into a single call.
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:13:import { isCocoIndexAvailable } from '../lib/utils/cocoindex-path.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:107:interface CocoIndexStatus {
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:115:  cocoIndex: CocoIndexStatus;
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:128:  cocoIndex: CocoIndexStatus;
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:141:  cocoIndex: CocoIndexStatus;
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:182:        title: 'CocoIndex Status',
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:609:  // ── Sub-call 3: CocoIndex availability (F046/F051: shared helper) ──
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:610:  const cocoIndex: CocoIndexStatus = {
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:611:    available: isCocoIndexAvailable(),
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:615:    hints.push('CocoIndex not installed. Install: `bash .opencode/skills/mcp-coco-index/scripts/install.sh`');
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts:707:      title: 'CocoIndex Status',
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/co-activation.ts:164: * Boost a search result's score based on co-activation with related memories.
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/co-activation.ts:276:    // Get the memory's embedding via a vector search for itself
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-metadata.vitest.ts:4:// From lib/search/anchor-metadata.ts, plus the Stage 2 wiring
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-metadata.vitest.ts:11:} from '../lib/search/anchor-metadata';
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-metadata.vitest.ts:12:import type { PipelineRow } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-metadata.vitest.ts:73:        'We decided to use RRF over BM25.',        // line 2
.opencode/skills/mcp-coco-index/manual_testing_playbook/06--error-handling/001-no-results-graceful-handling.md:3:description: "This scenario validates No results graceful handling for `ERR-001`. It focuses on Verify search returns empty results gracefully for a nonsense query (no crash, no error)."
.opencode/skills/mcp-coco-index/manual_testing_playbook/06--error-handling/001-no-results-graceful-handling.md:10:This scenario validates No results graceful handling for `ERR-001`. It focuses on Verify search returns empty results gracefully for a nonsense query (no crash, no error).
.opencode/skills/mcp-coco-index/manual_testing_playbook/06--error-handling/001-no-results-graceful-handling.md:19:- Objective: Verify search returns empty results gracefully for a nonsense query (no crash, no error)
.opencode/skills/mcp-coco-index/manual_testing_playbook/06--error-handling/001-no-results-graceful-handling.md:20:- Prompt: `As a manual-testing orchestrator, search for a completely nonsensical term that has no matches against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Response is valid (not an exception or error); result array is empty or contains zero entries; no stack trace. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/06--error-handling/001-no-results-graceful-handling.md:31:| ERR-001 | No results graceful handling | Verify search returns empty results gracefully for a nonsense query (no crash, no error) | `As a manual-testing orchestrator, search for a completely nonsensical term that has no matches against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Response is valid (not an exception or error); result array is empty or contains zero entries; no stack trace. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `mcp__cocoindex_code__search({ "query": "xyzzy_nonexistent_symbol_99999" })` -> 2. Verify response is a valid empty result (empty array or "no results" message, NOT an error or crash) | Response is valid (not an exception or error); result array is empty or contains zero entries; no stack trace | MCP tool output showing empty/zero results | PASS if empty results returned with no error; FAIL if tool throws an exception, crashes, or returns an error message | Check daemon logs for unhandled exceptions; verify index exists; test with `ccc search "xyzzy_nonexistent_symbol_99999" --limit 1` via CLI for comparison |
.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:65:type MemorySearchModule = typeof import('./memory-search.js');
.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:101:    memorySearchModule = loadHandlerModule<MemorySearchModule>('memory-search');
.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:211:// Memory search handlers
.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:213:export const handle_memory_search = lazyFunction(getMemorySearchModule, 'handle_memory_search');
.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:217:export const handle_memory_match_triggers = lazyFunction(getMemoryTriggersModule, 'handle_memory_match_triggers');
.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts:311:export const handle_memory_context = lazyFunction(getMemoryContextModule, 'handle_memory_context');
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/pressure-monitor.ts:4:// Feature catalog: Quality-aware 3-tier search fallback
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/temporal-contiguity.ts:4:// Boost search results when memories are temporally adjacent,
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/temporal-contiguity.ts:51: * Apply temporal-contiguity boost to vector search results.
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:16:import { isSessionBoostEnabled, isCausalBoostEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:17:import { executePipeline, type PipelineConfig } from '../search/pipeline/index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:62:  searchLimit?: number;
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:73:/** Build holdout candidate pools from the last 30 days of search traffic. */
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:79:/** Use the same top-k depth as normal interactive search responses. */
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:208:    WHERE event_type = 'search'
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:223:function buildReplayPipelineConfig(query: string, searchLimit: number): PipelineConfig {
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:226:    searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:227:    limit: searchLimit,
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:323:  searchLimit: number,
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:325:  const pipelineResult = await executePipeline(buildReplayPipelineConfig(queryText, searchLimit));
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:348:  searchLimit: number,
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:367:      const ranks = await replayQueryForShadowEvaluation(db, queryText, searchLimit);
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:403:  const searchLimit = options.searchLimit ?? DEFAULT_SEARCH_LIMIT;
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:424:      console.warn('[shadow-evaluation-runtime] skipped cycle: no recent search queries available');
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/shadow-evaluation-runtime.ts:428:    const replayed = await buildHoldoutReplayMap(db, queryRows, holdoutPercent, seed, searchLimit);
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:4:// Feature catalog: Trigger phrase matching (memory_match_triggers)
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:7:import * as vectorIndex from '../search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:198:  'research',
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:206:      (document_type IN ('spec', 'plan', 'tasks', 'checklist', 'decision_record', 'implementation_summary', 'research', 'handover')
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts:660:// Correction signals (0.2) weighted higher than preferences (0.1) and reinforcement (0.15) — corrections indicate stronger search intent
.opencode/skills/system-spec-kit/mcp_server/tests/pe-gating.vitest.ts:3:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/pe-gating.vitest.ts:31:describe('PE gating scoped similar-memory search', () => {
.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:82:    preferredTool: 'code_graph_query';
.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:349:    preferredTool: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts:350:    message: 'Advisory only: when the next question is about callers, imports, dependencies, or outline, prefer `code_graph_query` before Grep or Glob.',
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:25:// Vector-index-impl.js (SQL search ranking).
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:275:  research: 2.0,         // 2x stability — research context decays slower
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:281:      ([legacy, canonical]) => [legacy, canonical === 'planning' ? Infinity : canonical === 'research' ? 2.0 : 1.0]
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:318: * @param contextType    Continuity-row context_type field (e.g. "decision", "research")
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:378:      transient, implementation, discovery, research, general)
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:387: * Context types that should never decay under the hybrid decay policy.
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:402:  'research',
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:408: * REQ-D4-002: Check whether the hybrid decay policy feature flag is enabled.
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:417: * REQ-D4-002: Classify a memory's decay behaviour under the hybrid policy.
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/fsrs-scheduler.ts:440: * REQ-D4-002: Apply the hybrid decay policy to a stability value.
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/001-daemon-auto-start.md:28:- Prompt: `As a manual-testing orchestrator, stop the daemon, then search -- against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify auto-start against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: daemon stops or reports already stopped; Step 3: search returns at least 1 result; Step 5: daemon reports running. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/001-daemon-auto-start.md:29:- Expected signals: Step 1: daemon stops or reports already stopped; Step 3: search returns at least 1 result; Step 5: daemon reports running
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/001-daemon-auto-start.md:31:- Pass/fail: PASS if search succeeds after daemon stop (auto-restart) AND daemon status confirms running; FAIL if search fails or daemon remains stopped
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/001-daemon-auto-start.md:40:| DMN-001 | Daemon auto-start | Verify daemon starts automatically when a CLI command is issued after it has been stopped | `As a manual-testing orchestrator, stop the daemon, then search -- against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify auto-start against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: daemon stops or reports already stopped; Step 3: search returns at least 1 result; Step 5: daemon reports running. Return a concise user-facing pass/fail verdict with the main reason.` | 1. Confirm no other playbook scenario is running against the same daemon -> 2. `bash: ccc daemon stop` -> 3. `bash: sleep 2` -> 4. `bash: ccc search "test" --limit 1` -> 5. Verify search returns results (daemon restarted) -> 6. `bash: ccc daemon status` (confirm running) | Step 2: daemon stops or reports already stopped; Step 4: search returns at least 1 result; Step 6: daemon reports running | Transcript of all 6 steps; daemon status output | PASS if search succeeds after daemon stop (auto-restart) AND daemon status confirms running; FAIL if search fails or daemon remains stopped | Check `~/.cocoindex_code/daemon.pid` for stale PID; check `daemon.log` for startup errors; verify port/socket availability |
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/README.md:24:`lib/parsing/` turns markdown files into structured inputs for save, search, and trigger flows. The directory contains three focused modules:
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/README.md:28:- `content-normalizer.ts` for embedding/BM25-safe normalization.
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/README.md:38:| `content-normalizer.ts` | Strips frontmatter, anchors, HTML comments, fences, tables, list syntax, and heading markers before embedding or BM25 work |
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/README.md:49:- `content-normalizer.ts` is the shared normalization path for both embedding generation and BM25 token building.
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/README.md:55:- `../search/README.md`
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/002-daemon-status-inspection.md:20:- Prompt: `As a manual-testing orchestrator, check daemon status and against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify runtime files against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: output includes version or uptime information; Step 2: both daemon.pid and daemon.sock files exist. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/002-daemon-status-inspection.md:31:| DMN-002 | Daemon status inspection | Verify `ccc daemon status` shows version and uptime; PID and socket files exist | `As a manual-testing orchestrator, check daemon status and against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify runtime files against the current CocoIndex CLI, daemon, and MCP surfaces in this repository. Verify Step 1: output includes version or uptime information; Step 2: both daemon.pid and daemon.sock files exist. Return a concise user-facing pass/fail verdict with the main reason.` | 1. `bash: ccc daemon status` -> 2. `bash: ls ~/.cocoindex_code/daemon.pid ~/.cocoindex_code/daemon.sock` | Step 1: output includes version or uptime information; Step 2: both `daemon.pid` and `daemon.sock` files exist | Daemon status output; file listing | PASS if daemon status reports running AND both PID/socket files exist; PARTIAL if status reports running but one file missing; FAIL if daemon not running or both files missing | Run `ccc search "test" --limit 1` or `ccc index` to trigger daemon auto-start, then re-check status; inspect `daemon.log` for errors; verify `~/.cocoindex_code/` permissions |
.opencode/skills/system-spec-kit/mcp_server/handlers/mutation-hooks.ts:9:import { clearDegreeCache } from '../lib/search/graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:3:description: "Research-backed memory decay, retrieval, classification and lifecycle engine with document-aware scoring inputs."
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:12:> Research-backed memory decay, retrieval, classification and lifecycle engine with document-aware scoring inputs.
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:35:The cognitive subsystem implements human memory principles to manage conversation context intelligently. It models how memories decay and strengthen through use, then transition between activity states based on research-validated algorithms from cognitive science and spaced repetition systems. Retrieval consumes `documentType` and `specLevel` metadata from indexing, so cognitive scoring is applied to both memory notes and spec documents.
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:280:**Purpose**: Research-validated memory forgetting curve
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:543:// Populate related memories using vector search
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:653:**Purpose**: Boost search results by temporal proximity and query temporal neighbors. Also builds spec-folder timelines.
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:669:// Boost vector search results by temporal proximity
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:744:  candidates,        // from vector search
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:967:| [../search/vector-index.ts](../search/vector-index.ts)             | Semantic search using voyageai embeddings |
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:972:### External Research
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:977:| [Anki Research](https://faqs.ankiweb.net/what-spaced-repetition-algorithm.html) | Spaced repetition validation dataset                         |
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/README.md:996:*Cognitive Subsystem v1.9.0, Research-Backed Memory Management — Updated: 2026-02-27*
.opencode/skills/system-spec-kit/mcp_server/tests/memory-types.vitest.ts:118:        { path: '/project/.opencode/specs/008-feature/research/research.md', expected: 'semantic' },
.opencode/skills/system-spec-kit/mcp_server/tests/memory-types.vitest.ts:119:        { path: '/project/.opencode/specs/008-feature/research.md', expected: 'semantic' },
.opencode/skills/system-spec-kit/mcp_server/tests/memory-types.vitest.ts:121:        { path: '/project/.opencode/specs/008-feature/research/iterations/iteration-001.md', expected: 'working' },
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/memory-parser.ts:120:  'research': 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/memory-parser.ts:127:  'analysis': 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/memory-parser.ts:133:  'review': 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/parsing/memory-parser.ts:401:    'research.md': 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:2:// MODULE: CocoIndex Path Helper
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:4:// F046/F051: Shared helper for resolving the CocoIndex binary path.
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:12:/** Relative path from project root to the CocoIndex CLI binary. */
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:48: * Get the absolute path to the CocoIndex binary.
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:51:export function getCocoIndexBinaryPath(): string {
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:56: * Check whether the CocoIndex binary exists on disk.
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:58:export function isCocoIndexAvailable(): boolean {
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts:59:  return existsSync(getCocoIndexBinaryPath());
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/query-flow-tracker.ts:8:// Spec: system-spec-kit/023-hybrid-rag-fusion-refinement/014-feedback-signal-pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/query-flow-tracker.ts:148: * Call this after every search completion.
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/query-flow-tracker.ts:152: * @param query - The search query text
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/query-flow-tracker.ts:154: * @param shownMemoryIds - Memory IDs shown in this search's results
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/query-flow-tracker.ts:228: * Log `follow_on_tool_use` events for memories shown in a recent search.
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/query-flow-tracker.ts:229: * Call when any non-search tool is invoked within the follow-on window.
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/003-helper-script-readiness.md:27:- Real user request: `"Tell me whether this project is ready to run CocoIndex commands and bootstrap the daemon if it's not."`
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/003-helper-script-readiness.md:28:- Prompt: `As a manual-testing orchestrator, run doctor.sh --json --strict --require-config followed by ensure_ready.sh --json --strict --require-config against the current CocoIndex install in this repository. Verify both scripts exit 0 with healthy JSON; rerun ensure_ready.sh and confirm idempotency; then run both scripts from a temp directory with no .cocoindex_code/ to confirm --require-config makes them exit non-zero with an explicit reason. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/mcp-coco-index/manual_testing_playbook/04--daemon-lifecycle/003-helper-script-readiness.md:40:- Prompt: `As a manual-testing orchestrator, run doctor.sh --json --strict --require-config followed by ensure_ready.sh --json --strict --require-config against the current CocoIndex install in this repository. Verify both scripts exit 0 with healthy JSON; rerun ensure_ready.sh and confirm idempotency; then run both scripts from a temp directory with no .cocoindex_code/ to confirm --require-config makes them exit non-zero with an explicit reason. Return a concise user-facing pass/fail verdict with the main reason.`
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking-e2e.vitest.ts:26:import { executePipeline } from '../lib/search/pipeline/index.js';
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking-e2e.vitest.ts:34:vi.mock('../lib/search/session-boost.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking-e2e.vitest.ts:38:vi.mock('../lib/search/causal-boost.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking-e2e.vitest.ts:42:vi.mock('../lib/search/pipeline/index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking-e2e.vitest.ts:95:    ) VALUES (?, 'search', ?, 3, ?)
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking-e2e.vitest.ts:321:      searchLimit: 3,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:14:import * as intentClassifier from '../lib/search/intent-classifier.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:15:import type { IntentTelemetry } from '../lib/search/intent-classifier.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:17:// Query-intent routing (Phase 020: structural/semantic/hybrid classification)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:22:import { handleMemorySearch } from './memory-search.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:44:} from '../lib/search/session-transition.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:48:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:54:import { discoverSpecFolder, getSpecsBasePaths } from '../lib/search/folder-discovery.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:60:} from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:63:// Feature catalog: Unified context retrieval (memory_context)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:89:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:125:  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:128:  /** REQ-D5-003: Presentation profile ('quick'|'research'|'resume'|'debug'). Default: full response. */
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:217:  preferredTool: 'code_graph_query';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:442:    preferredTool: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:443:    message: 'Advisory only: this looks like a structural question. Prefer `code_graph_query` before Grep or Glob for callers, imports, outline, and dependency lookups.',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:564:            tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:576:            tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:593:          tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:604:          tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:901:  // Deep: Comprehensive semantic search with full context
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:904:    description: 'Semantic search with full context retrieval',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:905:    strategy: 'search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:909:  // Focused: Intent-specific search with optimized weights
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:912:    description: 'Intent-aware search with task-specific optimization',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:913:    strategy: 'intent-search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1036:    tool: 'memory_context_resume',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1321:    // backend channel selection only (structural / hybrid / semantic) and MUST
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1353:/** Handle memory_context tool — L1 orchestration layer that routes to optimal retrieval strategy.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1367:      tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1392:      tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1406:  // graph context for structural/hybrid queries. Entire block is
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1419:          : classification.intent === 'hybrid'
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1420:            ? 'hybrid'
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1454:      } else if (classification.intent === 'hybrid') {
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1467:          // Code graph unavailable — hybrid degrades to semantic-only
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1501:      tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1520:  const layerInfo: LayerInfo | null = layerDefs.getLayerInfo('memory_context');
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1588:  // Phase C: Intent-to-profile auto-routing for memory_context.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1595:        detectedIntent as import('../lib/search/intent-classifier.js').IntentType
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1645:      tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1652:        alternativeLayers: layerDefs.getRecommendedLayers('search')
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1663:      tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1760:    tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1767:      `For more granular control, use L2 tools: memory_search, memory_match_triggers`,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1874:      tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1875:      error: 'memory_context failed due to an internal error',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1897:const handle_memory_context = handleMemoryContext;
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:1900:  handle_memory_context,
.opencode/skills/system-spec-kit/mcp_server/tests/cross-encoder-extended.vitest.ts:3:import * as crossEncoder from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-encoder-extended.vitest.ts:4:import type { RerankDocument, RerankResult } from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-encoder-extended.vitest.ts:239:      const results = await crossEncoder.rerankCohere('search query', docs);
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/README.md:23:- `../search/README.md`
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cleanup-helpers.ts:1:import { get_error_message } from '../search/vector-index-types.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-list.ts:12:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-merge-operation.vitest.ts:466:        'title: "Research"',
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-merge-operation.vitest.ts:467:        'description: "Research fixture"',
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-merge-operation.vitest.ts:468:        'contextType: "research"',
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-merge-operation.vitest.ts:479:          '<!-- trailing research comment -->',
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-merge-operation.vitest.ts:485:        docPath: 'research.md',
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-merge-operation.vitest.ts:499:      expect(result.updatedDocument.trimEnd().endsWith('<!-- trailing research comment -->\n<!-- /ANCHOR:findings -->')).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-merge-operation.vitest.ts:509:        docPath: 'research.md',
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:2:// Converted from: t206-search-archival.test.ts (custom runner)
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:15:  path.join(SRC_LIB_PATH, 'search', 'vector-index-queries.ts'),
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:24:describe('T206 - vector_search accepts includeArchived [deferred - DB dependency]', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:26:    expect(VECTOR_INDEX_QUERIES_SOURCE).toContain('export { vector_search as vectorSearch };');
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:30:    expect(VECTOR_INDEX_QUERIES_SOURCE).toMatch(/export function vector_search\([\s\S]*?includeArchived = false/);
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:34:describe('T206 - multi_concept_search archival compatibility [deferred - DB dependency]', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:36:    expect(VECTOR_INDEX_QUERIES_SOURCE).toContain('export { multi_concept_search as multiConceptSearch };');
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:40:    expect(VECTOR_INDEX_QUERIES_SOURCE).toMatch(/export function multi_concept_search/);
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:41:    expect(VECTOR_INDEX_QUERIES_SOURCE).not.toMatch(/export function multi_concept_search\([\s\S]*?includeArchived = false/);
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:45:describe('T206 - keyword_search archival compatibility [deferred - DB dependency]', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:47:    expect(VECTOR_INDEX_QUERIES_SOURCE).toContain('export { keyword_search as keywordSearch };');
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:51:    expect(VECTOR_INDEX_QUERIES_SOURCE).toMatch(/export function keyword_search/);
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:52:    expect(VECTOR_INDEX_QUERIES_SOURCE).not.toMatch(/export function keyword_search\([\s\S]*?includeArchived = false/);
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:78:      path.join(SRC_LIB_PATH, 'search', 'vector-index-schema.ts'),
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:84:  it('T206-SRC3: hybrid-search does not gate structural search on is_archived', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:88:        path.join(SRC_LIB_PATH, 'search', 'hybrid-search.ts'),
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:94:        path.join(SRC_LIB_PATH, 'search', 'hybrid-search.js'),
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:103:      path.join(SRC_LIB_PATH, 'search', 'hybrid-search.ts'),
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:109:  it('T206-SRC5: memory-search handler references includeArchived', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:111:      path.join(SRC_HANDLERS_PATH, 'memory-search.ts'),
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:133:  it('T235-BH1: vector_search does not use the old WHERE-clause archive filter', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:144:    // vector_search and multi_concept_search, and referenced in other
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:147:    // At least 4: vector_search param, multi_concept_search param,
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:152:  it('T235-BH3: keyword_search does NOT accept includeArchived after cleanup', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:153:    // After the 026.018 cleanup, keyword_search does not have an
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:154:    // includeArchived parameter — it was removed because keyword search
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:157:      /export function keyword_search\([^)]*\)/
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:165:  it('T235-BH4: handler memory-search reads includeArchived from args and passes to search layer', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:167:      path.join(SRC_HANDLERS_PATH, 'memory-search.ts'),
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:172:    // And passes it to one of the search functions
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:174:    // At least 2 references: extraction from args + pass to search function
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:178:  it('T235-BH5: hybrid-search options type includes includeArchived field', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts:180:      path.join(SRC_LIB_PATH, 'search', 'hybrid-search.ts'),
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill-graph.json:1:{"schema_version": 1, "generated_at": "2026-04-26T07:02:59.657976+00:00", "skill_count": 22, "families": {"cli": ["cli-claude-code", "cli-codex", "cli-copilot", "cli-gemini", "cli-opencode"], "mcp": ["mcp-chrome-devtools", "mcp-clickup", "mcp-coco-index", "mcp-code-mode", "mcp-figma"], "sk-code": ["sk-code-full-stack", "sk-code-opencode", "sk-code-review", "sk-code-web"], "sk-deep": ["sk-deep-research", "sk-deep-review"], "sk-util": ["sk-doc", "sk-git", "sk-improve-agent", "sk-improve-prompt"], "system": ["skill-advisor", "system-spec-kit"]}, "adjacency": {"cli-claude-code": {"siblings": {"cli-codex": 0.5, "cli-copilot": 0.5, "cli-gemini": 0.5, "cli-opencode": 0.5}}, "cli-codex": {"siblings": {"cli-claude-code": 0.5, "cli-copilot": 0.5, "cli-gemini": 0.5, "cli-opencode": 0.5}}, "cli-copilot": {"siblings": {"cli-claude-code": 0.5, "cli-codex": 0.5, "cli-gemini": 0.5, "cli-opencode": 0.5}}, "cli-gemini": {"siblings": {"cli-claude-code": 0.5, "cli-codex": 0.5, "cli-copilot": 0.5, "cli-opencode": 0.5}}, "cli-opencode": {"siblings": {"cli-claude-code": 0.5, "cli-codex": 0.5, "cli-copilot": 0.5, "cli-gemini": 0.5}}, "mcp-chrome-devtools": {"depends_on": {"mcp-code-mode": 0.7}, "enhances": {"sk-code-web": 0.5}}, "mcp-clickup": {"depends_on": {"mcp-code-mode": 0.9}}, "mcp-coco-index": {"enhances": {"system-spec-kit": 0.3}, "prerequisite_for": {"skill-advisor": 0.7}}, "mcp-code-mode": {"prerequisite_for": {"mcp-figma": 0.9, "mcp-clickup": 0.9, "mcp-chrome-devtools": 0.7}}, "mcp-figma": {"depends_on": {"mcp-code-mode": 0.9}, "enhances": {"sk-code-web": 0.4}}, "sk-code-full-stack": {"enhances": {"sk-code-review": 0.3}, "siblings": {"sk-code-opencode": 0.4, "sk-code-web": 0.4}}, "sk-code-opencode": {"enhances": {"sk-code-review": 0.3}, "siblings": {"sk-code-full-stack": 0.4, "sk-code-web": 0.4}}, "sk-code-review": {"enhances": {"sk-code-opencode": 0.7, "sk-code-web": 0.7, "sk-code-full-stack": 0.7}, "prerequisite_for": {"sk-deep-review": 0.8}}, "sk-code-web": {"enhances": {"sk-code-review": 0.3}, "siblings": {"sk-code-opencode": 0.4, "sk-code-full-stack": 0.4}}, "sk-deep-research": {"siblings": {"sk-deep-review": 0.5}}, "sk-deep-review": {"depends_on": {"sk-code-review": 0.8}, "siblings": {"sk-deep-research": 0.5}}, "sk-doc": {"enhances": {"system-spec-kit": 0.5}, "siblings": {"sk-git": 0.4}}, "sk-git": {"siblings": {"sk-doc": 0.4}}, "sk-improve-agent": {"siblings": {"sk-improve-prompt": 0.4}}, "sk-improve-prompt": {"enhances": {"cli-claude-code": 0.4, "cli-codex": 0.4, "cli-copilot": 0.4, "cli-gemini": 0.4}, "siblings": {"sk-improve-agent": 0.4}}, "skill-advisor": {"depends_on": {"mcp-coco-index": 0.7}, "enhances": {"cli-claude-code": 0.7, "cli-codex": 0.7, "cli-copilot": 0.7, "cli-gemini": 0.7, "mcp-chrome-devtools": 0.7, "mcp-clickup": 0.7, "mcp-coco-index": 0.7, "mcp-code-mode": 0.7, "mcp-figma": 0.7, "sk-code-full-stack": 0.7, "sk-code-opencode": 0.7, "sk-code-review": 0.7, "sk-code-web": 0.7, "sk-deep-research": 0.7, "sk-deep-review": 0.7, "sk-doc": 0.7, "sk-git": 0.7, "sk-improve-agent": 0.7, "sk-improve-prompt": 0.7, "system-spec-kit": 0.7}}, "system-spec-kit": {"enhances": {"sk-doc": 0.4, "sk-git": 0.3, "sk-code-opencode": 0.3}}}, "signals": {"cli-claude-code": ["claude code", "claude cli", "delegate to claude"], "cli-codex": ["codex cli", "codex exec", "delegate to codex"], "cli-copilot": ["copilot cli", "delegate to copilot"], "cli-gemini": ["gemini cli", "delegate to gemini", "google search"], "cli-opencode": ["opencode cli", "opencode run", "delegate to opencode", "parallel detached session", "spec kit runtime"], "mcp-chrome-devtools": ["chrome devtools", "browser debug", "dom inspect", "lighthouse"], "mcp-clickup": ["clickup", "project management", "clickup task"], "mcp-coco-index": ["semantic search", "code search", "find code", "coco index"], "mcp-code-mode": ["code mode", "mcp tool", "call tool chain"], "mcp-figma": ["figma", "design file", "figma component", "figma export"], "sk-code-full-stack": ["full stack", "implement feature", "stack detection"], "sk-code-opencode": ["opencode", "system code", "mcp server code", "skill code"], "sk-code-review": ["code review", "pr review", "security review", "quality gate", "findings"], "sk-code-web": ["web code", "frontend", "webflow", "css standards"], "sk-deep-research": ["deep research", "research loop", "investigate"], "sk-deep-review": ["deep review", "review loop", "iterative review", "spec folder review"], "sk-doc": ["create readme", "write documentation", "install guide", "feature catalog"], "sk-git": ["git workflow", "worktree", "conventional commit", "pull request", "finish work"], "sk-improve-agent": ["improve agent", "evaluate agent", "agent scoring"], "sk-improve-prompt": ["improve prompt", "enhance prompt", "prompt framework", "clear score"], "skill-advisor": ["skill routing", "gate 2", "which skill", "route request"], "system-spec-kit": ["spec folder", "save context", "save memory", "spec kit", "memory search"]}, "conflicts": [], "hub_skills": ["cli-claude-code", "cli-codex", "cli-copilot", "cli-gemini", "cli-opencode", "mcp-code-mode", "sk-code-full-stack", "sk-code-opencode", "sk-code-review", "sk-code-web"], "topology_warnings": {}}
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/batch-learning.ts:124:import { isBatchLearnedFeedbackEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/manage/README.md:88:- `../search/graph-search-fn.ts` — typed-weighted degree scoring used by the live retrieval path.
.opencode/skills/system-spec-kit/mcp_server/tests/p0-b-reconsolidation-composite.vitest.ts:8:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/handlers/session-health.ts:184:    hints.push('No tool calls in >60 min. Consider calling `memory_context` to refresh session state.');
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:8:import type { GraphSearchFn } from '../lib/search/search-types.js';
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:42:/** Hybrid search module interface */
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:67:  hybridSearch?: HybridSearchLike;
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:100:let hybridSearch: HybridSearchLike | null = null;
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:163:  if (hybridSearch) {
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:165:      console.warn('[db-state] hybridSearch reinit missing graphSearchFn; graph retrieval channel is disabled');
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:167:    hybridSearch.init(database, vectorIndex?.vectorSearch, graphSearchFnRef ?? null);
.opencode/skills/system-spec-kit/mcp_server/core/db-state.ts:199:  if (deps.hybridSearch) hybridSearch = deps.hybridSearch;
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoints-extended.vitest.ts:20:type VectorIndexModule = typeof import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoints-extended.vitest.ts:73:      vectorIndexModule = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:26:export type TaskType = 'search' | 'browse' | 'modify' | 'checkpoint' | 'analyze' | 'maintenance' | 'default';
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:50:    tools: ['memory_context', 'session_resume', 'session_bootstrap']
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:55:    description: 'Primary memory operations. Use when you need specific search or save functionality.',
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:58:    useCase: 'Direct access to search, save, and trigger matching when L1 routing is not needed.',
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:59:    tools: ['memory_search', 'memory_quick_search', 'memory_save', 'memory_match_triggers']
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:104:      'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:105:      'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/layer-definitions.ts:220:    search: ['L1', 'L2'],
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/README.md:35:The telemetry module provides structured observability for the retrieval pipeline and scoring subsystem. It records per-stage latency, search mode selection, fallback triggers, composite quality scores, scoring observation samples, trace payload validation, and agent consumption events. Telemetry data flows to governance tooling and is used by retrieval handlers to surface pipeline health metrics.
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/README.md:83:| `consumption-logger.ts` | Logs agent consumption events (`search`, `context`, `triggers`) to SQLite `consumption_log` table; pattern detection for zero-result, high-frequency, and intent-mismatch queries |
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/README.md:143:**Purpose**: Capture which search mode was used and whether it was overridden.
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/README.md:147:| `selectedMode` | `string \| null` | Mode chosen for this run (e.g., `hybrid`, `auto`, `deep`) |
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/README.md:235:**Purpose**: Persist the spec-shaped session transition trace contract into retrieval telemetry when trace-enabled search paths emit transition metadata.
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/README.md:462:| [lib/search/README.md](../search/README.md) | Hybrid search pipeline |
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/README.md:470:| `handlers/memory-search.ts` | Primary integration point for telemetry collection |
.opencode/skills/system-spec-kit/mcp_server/lib/graph/contradiction-detection.ts:10:import { isTemporalEdgesEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts:14:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts:452:    hints.push('Vector search unavailable - fallback to BM25');
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts:454:  // FTS5 consistency check
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts:461:          `FTS5 index out of sync: memory_index has ${memoryCountRow.count} rows, memory_fts has ${ftsCountRow.count} rows. ` +
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts:462:          `Run memory_index_scan with force:true to rebuild FTS5 index.`
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts:477:              hints.push('Auto-repair completed: FTS5 index rebuilt and trigger cache refreshed.');
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts:494:      hints.push(`FTS5 consistency check failed: ${sanitizeErrorForHint(message)}`);
.opencode/skills/system-spec-kit/mcp_server/tests/causal-fixes.vitest.ts:5:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:50:| L2 | Core | 1500 | Primary memory operations (search, save, triggers) |
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:134:const budget = getTokenBudget('memory_search');
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:141:const enhanced = enhanceDescription('memory_search', 'Search memories');
.opencode/skills/system-spec-kit/mcp_server/lib/architecture/README.md:148:const layers = getRecommendedLayers('search');
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/eval-channel-tracking.ts:4:// Extracted from handlers/memory-search.ts
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/eval-channel-tracking.ts:59: * Falls back to `['hybrid']` if no channels are found.
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/eval-channel-tracking.ts:85:    channels.add('hybrid');
.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:53:  memory_search: ERROR_CODES.SEARCH_FAILED,
.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:54:  memory_quick_search: ERROR_CODES.SEARCH_FAILED,
.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:55:  memory_context: ERROR_CODES.SEARCH_FAILED,
.opencode/skills/system-spec-kit/mcp_server/lib/errors/core.ts:56:  memory_match_triggers: ERROR_CODES.SEARCH_FAILED,
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-parser.ts:12:import { extractKeywords } from '../search/folder-discovery.js';
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-parser.ts:43:  path.join('research', 'research.md'),
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-parser.ts:44:  'research.md',
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-parser.ts:52:  /^(spec\.md|plan\.md|tasks\.md|checklist\.md|decision-record\.md|implementation-summary\.md|research\.md|research\/research\.md|handover\.md|resource-map\.md)$/;
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-parser.ts:526:      !candidate.startsWith('./research/') &&
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-parser.ts:1217: * Convert graph metadata into a searchable text block for indexing.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/fixtures/skill_advisor_regression_cases.jsonl:17:{"id":"P1-SEARCH-002","priority":"P1","prompt":"semantic code search for rate limiting","confidence_only":false,"expect_result":true,"expected_top_any":["mcp-coco-index"],"expect_kind":"skill","allow_command_bridge":false}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/fixtures/skill_advisor_regression_cases.jsonl:18:{"id":"P1-RESEARCH-001","priority":"P1","prompt":"autoresearch this repository architecture","confidence_only":false,"expect_result":true,"expected_top_any":["sk-deep-research"],"expect_kind":"skill","allow_command_bridge":false}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/fixtures/skill_advisor_regression_cases.jsonl:19:{"id":"P1-RESEARCH-002","priority":"P1","prompt":"/autoresearch auth subsystem","confidence_only":false,"expect_result":true,"expected_top_any":["sk-deep-research"],"expect_kind":"skill","allow_command_bridge":false}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/fixtures/skill_advisor_regression_cases.jsonl:50:{"id":"P1-PHRASE-006","priority":"P1","prompt":"vector search","confidence_only":false,"expect_result":true,"expected_top_any":["mcp-coco-index"],"expect_kind":"skill","allow_command_bridge":false}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/fixtures/skill_advisor_regression_cases.jsonl:51:{"id":"P1-PHRASE-007","priority":"P1","prompt":"concept search","confidence_only":false,"expect_result":true,"expected_top_any":["mcp-coco-index"],"expect_kind":"skill","allow_command_bridge":false}
.opencode/skills/system-spec-kit/mcp_server/tests/eval-logger.vitest.ts:158:        query: 'hybrid search for memory retrieval',
.opencode/skills/system-spec-kit/mcp_server/tests/eval-logger.vitest.ts:276:  describe('eval_run_id consistency within a single search invocation', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/eval-logger.vitest.ts:387:    // A full end-to-end search takes 100-500ms, so 10ms headroom is well within 10%.
.opencode/skills/system-spec-kit/mcp_server/tests/eval-logger.vitest.ts:432:  it('T004b-3: observer effect relative overhead does not exceed 10% of a representative search baseline', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/eval-logger.vitest.ts:433:    // Simulate a representative "search baseline" time: 50ms (well within real search latency).
.opencode/skills/system-spec-kit/mcp_server/tests/eval-logger.vitest.ts:448:      logChannelResult({ evalRunId, queryId, channel: 'hybrid', resultMemoryIds: [1, 2], scores: [0.9, 0.8] });
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:3:description: "Core library modules for search, scoring, cognitive memory and storage."
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:12:> Core library modules for search, scoring, cognitive memory and storage.
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:36:The MCP Server Library provides the core functionality for the Spec Kit Memory MCP server. It implements cognitive memory features including semantic search, attention decay, importance scoring and intelligent context retrieval. These modules work together to provide AI assistants with human-like memory recall and context awareness.
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:44:| Module Categories | 28 | architecture, cache, chunking, code-graph, cognitive, config, contracts, errors, eval, extraction, feedback, governance, graph, interfaces, learning, manage, ops, parsing, providers, response, scoring, search, session, spec, storage, telemetry, utils, validation |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:56:| **Semantic Search** | Vector-based similarity search with SQLite vector index and hybrid keyword matching |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:60:| **Document-Type Scoring** | Document-aware ranking supports spec lifecycle docs (spec/plan/tasks/checklist/decision-record/implementation-summary/research/handover) |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:70:| **Learned Feedback** | R11 selection tracking boosts future searches (9 safeguards, 0.7x weight) |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:96:import { SQLiteVectorStore } from './search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:113:import { SQLiteVectorStore } from './search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:136:├── search/                     # Search and retrieval (62 modules)
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:137:│   ├── vector-index.ts         # Vector similarity search with SQLite
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:139:│   ├── hybrid-search.ts        # Combined semantic + keyword search + token budget
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:142:│   ├── bm25-index.ts           # BM25 lexical indexing
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:143:│   ├── sqlite-fts.ts           # SQLite FTS5 full-text search
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:152:│   ├── graph-search-fn.ts      # Typed-weighted degree computation (Sprint 1)
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:154:│   ├── search-flags.ts         # Search feature flags
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:239:│   ├── bm25-baseline.ts        # BM25 baseline measurement
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:318:| `search/vector-index.ts` | Core vector similarity search with RRF fusion |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:319:| `search/vector-index-impl.ts` | Core vector index implementation |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:320:| `search/reranker.ts` | Result reranking |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:321:| `search/bm25-index.ts` | BM25 lexical search indexing |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:322:| `search/cross-encoder.ts` | Cross-encoder semantic reranking |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:323:| `search/intent-classifier.ts` | 7 intent types classification |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:335:| `search/query-classifier.ts` | Query complexity routing (simple/moderate/complex) |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:336:| `search/confidence-truncation.ts` | Low-confidence tail removal (2x median gap) |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:337:| `search/dynamic-token-budget.ts` | Per-tier token budgets (1500/2500/4000) |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:338:| `search/graph-search-fn.ts` | Typed-weighted degree computation for RRF 5th channel |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:339:| `search/channel-representation.ts` | Min-representation R2 (QUALITY_FLOOR=0.005) |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:355:**Vector Index**: Semantic similarity search using Voyage AI embeddings
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:360:| **Usage** | `search.vectorIndex.search_memories(query, options)` |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:363:**Hybrid Search**: Combines semantic and keyword search for better recall
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:368:| **Usage** | `search.hybridSearch.search(query, options)` |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:373:**FSRS Power-Law Decay**: Research-backed forgetting curve using formula R(t,S) = (1 + (19/81) x t/S)^(-0.5) where 19/81 ~ 0.2346
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:515:- `lib/search/vector-index-impl.ts`: v13 migration adds `document_type` and `spec_level` columns and indexes.
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:529:import * as vectorIndex from './search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:574:// Combine semantic and keyword search
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:575:import { hybridSearch } from './search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:578:const results = await hybridSearch('TODO authentication', queryEmbedding, {
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:612:| Direct imports | `import { SQLiteVectorStore } from './search/vector-index';` | Focused module usage |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:628:**Symptom**: `Error: Cannot find module './search/vector-index'`
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:635:import { SQLiteVectorStore } from './search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:674:| Import errors | Use concrete module paths such as `./search/vector-index` |
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:683:import { SQLiteVectorStore } from './search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/README.md:718:| [Search Modules](./search/) | Vector index, hybrid search, fusion algorithms |
.opencode/skills/system-spec-kit/mcp_server/core/README.md:23:`core/` is the shared runtime foundation used by handlers, search modules, hooks, and formatters.
.opencode/skills/system-spec-kit/mcp_server/core/README.md:41:- Reconnect flows are mutex-protected so handlers and search modules can safely rebind their DB-backed dependencies after external updates.
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:10:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:11:import * as bm25Index from '../lib/search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:14:import { executeAutoPromotion } from '../lib/search/auto-promotion.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:15:import { recordSelection } from '../lib/search/learned-feedback.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:85:  searchMode?: string;
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:464:  // T102 FIX: Rebuild search indexes after checkpoint restore
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:465:  // Without this, restored memories are invisible to search until server restart.
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:644:    searchMode,
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts:722:      searchMode,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/negative-feedback.ts:45:/** Index to keep per-memory lookups fast in search scoring. */
.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:32:The errors subsystem provides standardized error handling for the Spec Kit Memory MCP server. Every error includes a code and message paired with actionable recovery guidance to help agents self-diagnose and resolve issues across memory operations and document-aware indexing/search paths.
.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:40:| Tool-Specific Hints | 6 tools | memory_search, checkpoint_restore, memory_save, memory_index_scan, memory_drift_why, memory_causal_link |
.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:133:  return buildErrorResponse('memory_search', error, { query });
.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:143:const hint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:144:// Returns tool-specific hint for embedding failure in search context
.opencode/skills/system-spec-kit/mcp_server/lib/errors/README.md:147:// ['BM25 text search will still return relevant results', ...]
.opencode/skills/system-spec-kit/mcp_server/lib/graph/community-detection.ts:7:import { isCommunitySummariesEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/retrieval-telemetry.ts:19:import type { SessionTransitionTrace } from '../search/session-transition.js';
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/mpab-aggregation.ts:8:// Runtime pipeline gating uses isDocscoreAggregationEnabled() in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/mpab-aggregation.ts:67: * explicitly set to "false". Runtime pipeline gating uses search-flags
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/consumption-logger.ts:21:export type ConsumptionEventType = 'search' | 'context' | 'triggers';
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-signals.ts:14:} from '../search/pipeline/ranking-contract.js';
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-signals.ts:553: * Apply graph signal adjustments to scored search result rows.
.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:4:// Dispatch for L1 Orchestration tool: memory_context (T303).
.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:11:export const TOOL_NAMES = new Set(['memory_context']);
.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts:16:    case 'memory_context': return handleMemoryContext(parseArgs<ContextArgs>(validateToolArgs('memory_context', args)));
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:145:    hint: 'Embedding generation failed. Search will fall back to BM25 text matching.',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:337:      'If vector search failed, results may still include BM25 matches'
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:343:    hint: 'Vector search unavailable. Using text-based search as fallback.',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:347:      'Text search (BM25) will still work for keyword matches'
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:357:      'Use memory_match_triggers() for prompt-based matching instead'
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:360:    toolTip: 'memory_match_triggers()'
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:366:      'Or use concepts array for multi-concept search',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:375:      'Try broader search terms',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:376:      'Remove specFolder filter to search all memories',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:539:      'Check memory_search() for existing similar content'
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:693:  // Memory_search specific hints
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:694:  memory_search: {
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:696:      hint: 'Semantic search unavailable. Results limited to keyword matching.',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:698:        'BM25 text search will still return relevant results',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:700:        'Try memory_match_triggers() for trigger-based matching'
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:703:      toolTip: 'memory_match_triggers()'
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:706:      hint: 'Vector index not ready. Using text search.',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:753:      hint: 'Memory saved but embedding failed. Will be searchable via text only.',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:755:        'Memory is indexed and searchable via BM25 text search',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:777:      hint: 'Scan complete but embeddings unavailable. Files indexed for text search only.',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:779:        'Configure an embedding provider for semantic search',
.opencode/skills/system-spec-kit/mcp_server/lib/errors/recovery-hints.ts:781:        'Text search will work for all indexed files'
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:28:vi.mock('../lib/search/vector-index', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:141:  vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1029:  it('EXT-S8: Stats exposes graph channel metrics from hybrid-search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1032:    const hybridSearch = await import('../lib/search/hybrid-search');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1037:    expect(parsed?.data?.graphChannelMetrics).toEqual(hybridSearch.getGraphMetrics());
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1285:  it('EXT-H7: Health completes without vector search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1419:  it('EXT-H12: autoRepair rebuilds FTS drift and records repair metadata', async (ctx) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1486:  it('EXT-H13: autoRepair marks partial success when FTS mismatch remains but orphan cleanup succeeds', async (ctx) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1563:  it('EXT-H14: autoRepair marks partial success when FTS consistency check throws but orphan cleanup succeeds', async (ctx) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1577:    // Make the FTS consistency check throw before any repair attempt
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-extended.vitest.ts:1580:        get: () => { throw new Error('FTS5 table corrupted'); },
.opencode/skills/system-spec-kit/mcp_server/handlers/README.md:30:- `memory-search.ts` - L2 hybrid search handler with telemetry and profile support.
.opencode/skills/system-spec-kit/mcp_server/handlers/README.md:45:- `code-graph/query.ts` - `code_graph_query`: query structural relationships (outline, calls, imports).
.opencode/skills/system-spec-kit/mcp_server/handlers/README.md:47:- `code-graph/context.ts` - `code_graph_context`: LLM-oriented compact graph neighborhoods.
.opencode/skills/system-spec-kit/mcp_server/handlers/README.md:70:- `memory-crud-health.ts` surfaces embedding retry stats and FTS/index sync diagnostics as part of the health response.
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:42:      { source: SOURCE_TYPES.BM25, results: bm25Results },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:83:      { id: 'bm25-only', title: 'BM25 Only' },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:88:      { source: SOURCE_TYPES.BM25, results: bm25Results },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:105:      { source: SOURCE_TYPES.BM25, results: [] },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:141:      { id: 'b1', title: 'BM25 Result 1' },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:147:      { source: SOURCE_TYPES.BM25, results: bm25Results },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:155:    expect(b1.sources).toContain(SOURCE_TYPES.BM25);
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:160:    expect(shared.sources).toContain(SOURCE_TYPES.BM25);
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:162:    expect(shared.sourceScores).toHaveProperty(SOURCE_TYPES.BM25);
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:163:    expect(shared.sourceScores[SOURCE_TYPES.BM25]).toEqual(expect.any(Number));
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:169:      { source: SOURCE_TYPES.BM25, results: [{ id: '42', title: 'String' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:175:    expect(fused[0].sources).toContain(SOURCE_TYPES.BM25);
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:188:      { source: SOURCE_TYPES.BM25, results: bm25Results },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:204:      { source: SOURCE_TYPES.BM25, results: resultsB },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:235:      { source: SOURCE_TYPES.BM25, results: [{ id: 'b', title: 'B' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:302:      { source: SOURCE_TYPES.BM25, results: [
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:362:      { source: SOURCE_TYPES.BM25, results: [{ id: 'shared', title: 'Shared' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts:381:      { source: SOURCE_TYPES.BM25, results: [{ id: 'b1', title: 'BM25 1' }], weight: Number.POSITIVE_INFINITY },
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/confidence-tracker.ts:101: *   establishing durable feedback state for search-stage signal consumers.
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/confidence-tracker.ts:103: *   `recordNegativeFeedbackEvent`, and Stage 2 (`search/pipeline/stage2-fusion.ts`)
.opencode/skills/system-spec-kit/mcp_server/tests/graph-aware-stop.vitest.ts:61:  it('emits the canonical top-level score from the live research handler output', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-aware-stop.vitest.ts:67:    const sessionId = 'research-stop-live';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-aware-stop.vitest.ts:71:      loopType: 'research',
.opencode/skills/system-spec-kit/mcp_server/tests/graph-aware-stop.vitest.ts:91:      loopType: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/graph/README.md:42:- **Graph signals** compute two additive score bonuses for search results: momentum (recent degree change) and causal depth (normalized longest-path depth on the SCC-condensed causal DAG).
.opencode/skills/system-spec-kit/mcp_server/lib/graph/README.md:56:| Co-retrieval boost capped at 3 | Prevents community members from overwhelming primary search results. Boost factor of 0.3x was chosen empirically. |
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index-discovery.ts:74: * implementation-summary.md, research.md (incl. research/research.md),
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:5:{"id":"rr-iter2-005","bucket":"true_write","source_type":"paraphrased-realistic","prompt":"Fix the broken JSON example in `deep-research-config.json` and revalidate the packet.","gate3_triggers":"yes","gate3_reason_category":"file_write","skill_top_1":"system-spec-kit","skill_correct":"yes","notes":"config edit inside spec workflow"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:14:{"id":"rr-iter2-014","bucket":"true_read_only","source_type":"paraphrased-realistic","prompt":"Inspect the deep-research state log and summarize iteration progression.","gate3_triggers":"no","gate3_reason_category":"read_only","skill_top_1":"none","skill_correct":"no","notes":"inspection without modification"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:18:{"id":"rr-iter2-018","bucket":"true_read_only","source_type":"synthetic-realistic","prompt":"Explain the difference between `resume` and `restart` in deep-research lineage.","gate3_triggers":"no","gate3_reason_category":"read_only","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"deep-research concept question"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:24:{"id":"rr-iter2-024","bucket":"memory_save_resume","source_type":"synthetic-realistic","prompt":"Resume deep research on the routing-accuracy packet from the active lineage.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"resume phrase that produces new state"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:25:{"id":"rr-iter2-025","bucket":"memory_save_resume","source_type":"synthetic-realistic","prompt":"Continue iteration 7 and append the next delta record.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"continuation phrase with append behavior"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:28:{"id":"rr-iter2-028","bucket":"memory_save_resume","source_type":"synthetic-edge","prompt":"Resume iteration from the last state log entry, then continue the overnight run.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"implicit continuation wording"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:40:{"id":"rr-iter2-040","bucket":"mixed_ambiguous","source_type":"synthetic-edge","prompt":"Decompose the research plan only; do not touch packet files.","gate3_triggers":"no","gate3_reason_category":"mixed_ambiguous","skill_top_1":"none","skill_correct":"no","notes":"decompose token without write intent"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:41:{"id":"rr-iter2-041","bucket":"deep_loop_prompts","source_type":"synthetic-command","prompt":"Run `/spec_kit:deep-research :auto` on the routing-accuracy phase for 15 iterations.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"deep-research workflow creates packet artifacts"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:42:{"id":"rr-iter2-042","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Continue the active deep-research lineage with another routing-accuracy iteration.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"continuation of write-producing loop"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:45:{"id":"rr-iter2-045","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Run a fresh deep-research pass on the external evidence tree and write the iteration artifacts.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"explicit deep-loop write behavior"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:47:{"id":"rr-iter2-047","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Kick off an overnight research loop that populates `research/iterations/` and `deltas/`.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"artifact-producing loop"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:49:{"id":"rr-iter2-049","bucket":"deep_loop_prompts","source_type":"synthetic-edge","prompt":"Use the deep-research workflow, not a manual loop, to investigate routing drift.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"workflow selection still implies write-producing run"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:51:{"id":"rr-iter2-051","bucket":"skill_routing_prompts","source_type":"synthetic-realistic","prompt":"Find code that does vector-search blending when Grep is not enough.","gate3_triggers":"no","gate3_reason_category":"skill_routing_only","skill_top_1":"mcp-coco-index","skill_correct":"yes","notes":"semantic search request"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:60:{"id":"rr-iter2-060","bucket":"skill_routing_prompts","source_type":"synthetic-realistic","prompt":"Investigate the deep-research state with semantic search before opening files manually.","gate3_triggers":"no","gate3_reason_category":"skill_routing_only","skill_top_1":"mcp-coco-index","skill_correct":"yes","notes":"search-first exploration request"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:61:{"id":"rr-iter3-061","bucket":"true_write","source_type":"synthetic-realistic","prompt":"Add a packet-local helper that formats Gate 3 confusion-matrix rows for the research summary.","gate3_triggers":"yes","gate3_reason_category":"file_write","skill_top_1":"sk-code-opencode","skill_correct":"yes","notes":"direct helper implementation"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:62:{"id":"rr-iter3-062","bucket":"true_write","source_type":"synthetic-realistic","prompt":"Update `deep-research-dashboard.md` to show corpus-completion progress for routing accuracy.","gate3_triggers":"yes","gate3_reason_category":"file_write","skill_top_1":"system-spec-kit","skill_correct":"yes","notes":"dashboard markdown edit"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:74:{"id":"rr-iter3-074","bucket":"true_write","source_type":"synthetic-realistic","prompt":"Edit `research.md` to add a short section summarizing Gate 3 baseline accuracy.","gate3_triggers":"yes","gate3_reason_category":"file_write","skill_top_1":"system-spec-kit","skill_correct":"yes","notes":"research synthesis write"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:84:{"id":"rr-iter3-084","bucket":"true_read_only","source_type":"synthetic-realistic","prompt":"Audit the first two iterations for drift against the original research charter.","gate3_triggers":"no","gate3_reason_category":"read_only","skill_top_1":"sk-code-review","skill_correct":"yes","notes":"packet audit only"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:98:{"id":"rr-iter3-098","bucket":"true_read_only","source_type":"synthetic-realistic","prompt":"Review the deep-research instructions and confirm whether first-100 scoring is in scope.","gate3_triggers":"no","gate3_reason_category":"read_only","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"workflow inspection"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:99:{"id":"rr-iter3-099","bucket":"true_read_only","source_type":"paraphrased-realistic","prompt":"Explain why deep-loop prompts belong in the same corpus as ordinary file-write prompts.","gate3_triggers":"no","gate3_reason_category":"read_only","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"conceptual explanation"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:108:{"id":"rr-iter3-108","bucket":"memory_save_resume","source_type":"synthetic-realistic","prompt":"Resume deep research on the routing-accuracy phase and keep the active lineage.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"resume research flow"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:110:{"id":"rr-iter3-110","bucket":"memory_save_resume","source_type":"synthetic-realistic","prompt":"Continue iteration 8 of the routing-accuracy research wave.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"continue iteration phrasing"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:113:{"id":"rr-iter3-113","bucket":"memory_save_resume","source_type":"synthetic-edge","prompt":"Resume iteration from the latest JSONL state entry and append the next delta.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"resume from state log"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:118:{"id":"rr-iter3-118","bucket":"memory_save_resume","source_type":"synthetic-realistic","prompt":"Resume deep research from the active lineage and keep writing iteration artifacts.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"lineage resume"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:119:{"id":"rr-iter3-119","bucket":"memory_save_resume","source_type":"synthetic-edge","prompt":"Continue iteration after reloading the routing packet from continuity state.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"continue after continuity reload"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:121:{"id":"rr-iter3-121","bucket":"memory_save_resume","source_type":"paraphrased-realistic","prompt":"Can you resume the phase folder so the next research pass starts from the right lineage?","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"system-spec-kit","skill_correct":"yes","notes":"phase resume wording"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:125:{"id":"rr-iter3-125","bucket":"memory_save_resume","source_type":"synthetic-edge","prompt":"Continue iteration 11 and append the canonical JSONL line before anything else.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"continue-iteration exact phrase"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:126:{"id":"rr-iter3-126","bucket":"memory_save_resume","source_type":"synthetic-realistic","prompt":"Resume deep research for the routing hardening packet from the active state.","gate3_triggers":"yes","gate3_reason_category":"resume_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"resume deep research wording"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:129:{"id":"rr-iter3-129","bucket":"mixed_ambiguous","source_type":"paraphrased-realistic","prompt":"Explain the current resume handling, then write the approved summary into `research.md`.","gate3_triggers":"yes","gate3_reason_category":"mixed_ambiguous","skill_top_1":"system-spec-kit","skill_correct":"yes","notes":"explain plus write"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:134:{"id":"rr-iter3-134","bucket":"mixed_ambiguous","source_type":"synthetic-edge","prompt":"Explain whether the packet needs another phase or just continue the current research.","gate3_triggers":"no","gate3_reason_category":"mixed_ambiguous","skill_top_1":"system-spec-kit","skill_correct":"yes","notes":"workflow question only"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:149:{"id":"rr-iter3-149","bucket":"deep_loop_prompts","source_type":"synthetic-command","prompt":"Run `/spec_kit:deep-research :auto` for the routing hardening packet and stop on convergence.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"canonical deep-research command"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:150:{"id":"rr-iter3-150","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Start an overnight deep research run that keeps appending iteration markdown and delta JSONL files.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"overnight write-producing loop"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:152:{"id":"rr-iter3-152","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Continue the deep-research lineage with five more routing iterations.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"iteration continuation"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:153:{"id":"rr-iter3-153","bucket":"deep_loop_prompts","source_type":"synthetic-edge","prompt":"Launch a convergence-tracked research loop on Gate 3 misses instead of doing a manual pass.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"workflow-owned loop"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:156:{"id":"rr-iter3-156","bucket":"deep_loop_prompts","source_type":"paraphrased-realistic","prompt":"Run a fresh deep-research pass focused on prompt-routing false positives.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"fresh deep-research pass"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:157:{"id":"rr-iter3-157","bucket":"deep_loop_prompts","source_type":"synthetic-edge","prompt":"Use the deep-research workflow, not ad hoc notes, to keep iterating on routing accuracy.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"skill-owned loop selection"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:159:{"id":"rr-iter3-159","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Continue the current research loop and append the canonical state entry when the pass finishes.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"loop continuation"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:160:{"id":"rr-iter3-160","bucket":"deep_loop_prompts","source_type":"synthetic-edge","prompt":"Begin a 10-iteration research sweep over skill-routing prompts and record every pass.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"explicit iterative sweep"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:162:{"id":"rr-iter3-162","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Resume deep research on the routing packet and keep writing into `research/iterations/`.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"resume research loop"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:163:{"id":"rr-iter3-163","bucket":"deep_loop_prompts","source_type":"synthetic-edge","prompt":"Run another automated research cycle for the routing corpus and preserve the same lineage.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"automated research cycle"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:165:{"id":"rr-iter3-165","bucket":"deep_loop_prompts","source_type":"paraphrased-realistic","prompt":"Continue the overnight research run with one more packet-local iteration.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"overnight continuation"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:167:{"id":"rr-iter3-167","bucket":"deep_loop_prompts","source_type":"synthetic-realistic","prompt":"Launch a fresh routing-accuracy research loop that rebuilds state under the research folder.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"fresh loop with artifacts"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:168:{"id":"rr-iter3-168","bucket":"deep_loop_prompts","source_type":"synthetic-command","prompt":"Run `/spec_kit:deep-research :auto --max-iterations=8` on the routing packet.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"command with option"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:170:{"id":"rr-iter3-170","bucket":"deep_loop_prompts","source_type":"synthetic-edge","prompt":"Start a looped investigation into the `review + write` false-negative class and keep per-iteration artifacts.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"looped investigation"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:171:{"id":"rr-iter3-171","bucket":"deep_loop_prompts","source_type":"paraphrased-realistic","prompt":"Continue the current deep-research wave and append the next markdown iteration report.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"iteration report append"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:173:{"id":"rr-iter3-173","bucket":"deep_loop_prompts","source_type":"synthetic-edge","prompt":"Use the deep-research workflow to keep digging until newInfoRatio drops below the threshold.","gate3_triggers":"yes","gate3_reason_category":"deep_loop_write","skill_top_1":"sk-deep-research","skill_correct":"yes","notes":"threshold-governed research"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:175:{"id":"rr-iter3-175","bucket":"skill_routing_prompts","source_type":"synthetic-realistic","prompt":"Use semantic code search to find where Gate 3 resumes are handled.","gate3_triggers":"no","gate3_reason_category":"skill_routing_only","skill_top_1":"mcp-coco-index","skill_correct":"yes","notes":"semantic search only"}
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/labeled-prompts.jsonl:190:{"id":"rr-iter3-190","bucket":"skill_routing_prompts","source_type":"synthetic-realistic","prompt":"Use semantic search before Grep to find routing logic for continuity writes.","gate3_triggers":"no","gate3_reason_category":"skill_routing_only","skill_top_1":"mcp-coco-index","skill_correct":"yes","notes":"search-first request"}
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:4:// Combines vector, FTS, and BM25 search with fallback
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:16:import { DEGREE_CHANNEL_WEIGHT } from './graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:25:} from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:27:import { computeDegreeScores } from './graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:28:import type { GraphSearchFn } from './search-types.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:30:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:32:export type { GraphSearchFn } from './search-types.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:48:import { resolveFusionIntentContract } from './search-utils.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:98:   * enable all retrieval channels for this search call.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:119:   * - `'bm25'` — BM25 term-frequency relevance (min-max normalized per source group)
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:120:   * - `'fts'` — FTS5 rank score (absolute value, min-max normalized per source group)
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:123:   * After hybrid merge, all source scores are min-max normalized to 0-1 within
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:142:  const primarySource = result.sources[0] ?? 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:156: * Optional metadata about pipeline stages attached to enhanced search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:235:/** Primary vector similarity floor for hybrid fallback passes (percentage units). */
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:304: * Initialize hybrid search with database, vector search, and optional graph search dependencies.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:305: * @param database - The better-sqlite3 database instance for FTS and graph queries.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:306: * @param vectorFn - Optional vector search function for semantic similarity.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:307: * @param graphFn - Optional graph search function for causal/structural retrieval.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:319:// 8. BM25 SEARCH
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:322: * Search the BM25 index with optional spec folder filtering.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:323: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:325: * @returns Array of BM25-scored results tagged with source 'bm25'.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:332:    console.warn('[hybrid-search] BM25 not enabled — returning empty bm25Search results');
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:340:    const results = index.search(query, limit);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:342:    // BM25 document IDs are stringified
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:348:    // resolution returns [] rather than leaking unscoped BM25 candidates.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:353:        console.warn('[BM25] Spec-folder scope lookup failed, returning empty scoped results:', error);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:371:        console.warn('[BM25] Spec-folder scope lookup failed, returning empty scoped results:', error);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:380:        console.warn('[BM25] Spec-folder scope lookup failed, returning empty scoped results:', error);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:399:    console.warn(`[hybrid-search] BM25 search failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:405: * Check whether the BM25 index is populated and available for search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:406: * @returns True if the BM25 index exists and contains at least one document.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:422:// 9. FTS SEARCH
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:425: * Check whether the FTS5 full-text search table exists in the database.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:430:    console.warn('[hybrid-search] db not initialized — isFtsAvailable returning false');
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:446: * Run FTS5 full-text search with weighted BM25 scoring and optional spec folder filtering.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:447: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:449: * @returns Array of FTS-scored results tagged with source 'fts'.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:456:    console.warn('[hybrid-search] db not initialized or FTS unavailable — returning empty ftsSearch results');
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:463:    // C138-P2: Delegate to weighted BM25 FTS5 search from sqlite-fts.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:477:    console.warn(`[hybrid-search] FTS search failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:485: * Merge FTS and BM25 search results, deduplicating by ID and preferring FTS scores.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:486: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:497:  // Merge by canonical ID, prefer FTS scores.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:601:    source: typeof primary.source === 'string' ? primary.source : (sources[0] ?? 'hybrid'),
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:814:    : await hybridSearch(query, embedding, primaryOptions);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:836:      : await hybridSearch(query, embedding, retryOptions);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:856:      : await hybridSearch(query, embedding, retryOptions);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:875: * Run multi-channel hybrid search combining vector, FTS, BM25, and graph results with per-source normalization.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:876: * Prefer hybridSearchEnhanced() or searchWithFallback() instead. This function uses naive per-source
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:877: * min-max normalization which produces different orderings than the RRF pipeline in hybridSearchEnhanced().
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:880:async function hybridSearch(
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:898:  // Vector search
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:918:      console.warn(`[hybrid-search] Vector search failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:922:  // FTS search
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:928:  // BM25 search
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:934:  // Graph search
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:948:      console.warn(`[hybrid-search] Graph search failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1000: * Enhanced hybrid search with RRF fusion.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1001: * All search channels use synchronous better-sqlite3; sequential execution
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1004:async function hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1018:  return hybridSearch(query, embedding, options);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1117:        console.warn('[hybrid-search] Channel error:', _err instanceof Error ? _err.message : String(_err));
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1121:    // FTS channel (internal error handling in ftsSearch) — gated by query-complexity routing
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1125:        // FTS weight reduced to 0.3 after ablation showed 0.8 was harmful,
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1131:    // BM25 channel (internal error handling in bm25Search) — gated by query-complexity routing
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1135:        // BM25 weight 0.6 is lowest lexical channel — in-memory BM25 index
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1136:        // Has less precise scoring than SQLite FTS5 BM25; kept for coverage breadth.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1160:        console.warn('[hybrid-search] Channel error:', _err instanceof Error ? _err.message : String(_err));
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1204:        console.warn('[hybrid-search] Channel error:', _err instanceof Error ? _err.message : String(_err));
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1249:    // weights, avoiding the heavier hybridAdaptiveFuse() standard-first path.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1335:    console.warn(`[hybrid-search] Enhanced search failed, falling back: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1394:      console.error('[hybrid-search] MPAB error (non-fatal):', msg);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1417:      fusedHybridResults.map(r => ({ ...r, source: r.source || 'hybrid' })),
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1432:    console.warn('[hybrid-search] channel enforcement failed:', err instanceof Error ? err.message : String(err));
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1526:        console.warn(`[hybrid-search] MMR embedding retrieval failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1558:      console.warn('[hybrid-search] co-activation enrichment failed:', err instanceof Error ? err.message : String(err));
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1612:      console.warn('[hybrid-search] confidence truncation failed:', err instanceof Error ? err.message : String(err));
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1680:      queryId: `hybrid-${Date.now()}`,
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1736: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1737: * @param embedding - Optional embedding vector for semantic search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1738: * @param options - Hybrid search configuration options.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1783:  console.warn('[hybrid-search] Raw candidate collection returned empty results');
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1790: * fallback (searchWithFallbackTiered). Otherwise: C138-P0 two-pass adaptive
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1793: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1794: * @param embedding - Optional embedding vector for semantic search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1795: * @param options - Hybrid search configuration options.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1798:async function searchWithFallback(
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1805:    return searchWithFallbackTiered(query, embedding, options);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1810:  // P3-03 FIX: Use hybridSearchEnhanced (with RRF fusion) instead of
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1811:  // The naive hybridSearch that merges raw scores
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1827:  // Fallback to FTS only
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1833:  // Fallback to BM25 only
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1839:  console.warn('[hybrid-search] All search methods returned empty results');
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1846: * PI-A2: Last-resort structural search against the memory_index table.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1857:    console.warn('[hybrid-search] db not initialized — returning empty structuralSearch results');
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1911:    console.warn(`[hybrid-search] Structural search failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1969:// Memoize description map to avoid rebuilding on every search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1972:// Blocking the search hot path with synchronous filesystem crawls.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2157: * PI-A2: Quality-aware 3-tier search fallback chain.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2159: * TIER 1: hybridSearchEnhanced at minSimilarity=30
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2162: * TIER 2: hybridSearchEnhanced at minSimilarity=10, all allowed channels forced
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2170: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2171: * @param embedding - Optional embedding vector for semantic search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2172: * @param options - Hybrid search configuration options.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2175:async function searchWithFallbackTiered(
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2200:  // TIER 2: Widen search — lower similarity, force all channels
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2203:  console.error(`[hybrid-search] Tier 1→2 degradation: ${tier1Trigger.reason} (topScore=${tier1Trigger.topScore.toFixed(3)}, count=${tier1Trigger.resultCount})`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2227:  // TIER 3: Structural search (pure SQL last-resort)
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2230:  console.error(`[hybrid-search] Tier 2→3 degradation: ${tier2Trigger.reason} (topScore=${tier2Trigger.topScore.toFixed(3)}, count=${tier2Trigger.resultCount})`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2319: * @param result - The search result to measure.
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2446:      `[hybrid-search] Token budget overflow (single-result fallback): ` +
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2483:      `[hybrid-search] Token budget overflow (top-result fallback): ` +
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2500:    `[hybrid-search] Token budget overflow: ${totalTokens} tokens > ${effectiveBudget} budget, ` +
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2529:  hybridSearch,
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2530:  hybridSearchEnhanced,
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:2531:  searchWithFallback,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/README.md:43:| **6-Tier Importance** | Constitutional (always surface) to deprecated (hidden from search) |
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/README.md:100:| **deprecated** | 0.1 | 0.0x | No | Never | Hidden from search |
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/README.md:113:The scoring layer includes document-type multipliers for active document types (for example `spec`, `plan`, `tasks`, `checklist`, `decision-record`, `implementation-summary`, `memory`, `constitutional`, `research`, `handover`, `scratch`). These multipliers are used by folder scoring and document retrieval ranking.
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/README.md:227:// Returns: { value: 1.0, searchBoost: 3.0, decay: false, alwaysSurface: true, ... }
.opencode/skills/system-spec-kit/mcp_server/tests/memory-lineage-backfill.vitest.ts:7:import { createSchema, ensureSchemaVersion } from '../lib/search/vector-index-schema';
.opencode/skills/system-spec-kit/mcp_server/tests/stage2b-enrichment-extended.vitest.ts:8:vi.mock('../lib/search/anchor-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2b-enrichment-extended.vitest.ts:12:vi.mock('../lib/search/validation-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2b-enrichment-extended.vitest.ts:16:import { executeStage2bEnrichment } from '../lib/search/pipeline/stage2b-enrichment';
.opencode/skills/system-spec-kit/mcp_server/tools/types.ts:39:  profile?: 'quick' | 'research' | 'resume' | 'debug';
.opencode/skills/system-spec-kit/mcp_server/tools/types.ts:42:/** Arguments for memory search requests. */
.opencode/skills/system-spec-kit/mcp_server/tools/types.ts:141:  searchMode?: string;
.opencode/skills/system-spec-kit/mcp_server/tools/types.ts:159:    | 'research_finding'
.opencode/skills/system-spec-kit/mcp_server/lib/graph/usage-tracking.ts:10:import { isUsageRankingEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/session-learning.ts:4:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/routing-accuracy/score-routing-corpus.py:116:            re.search(rf"\b{re.escape(token)}\b", prompt_lower)
.opencode/skills/system-spec-kit/mcp_server/lib/enrichment/passive-enrichment.ts:129:      return ['[session] Context quality is CRITICAL. Consider running `memory_context({ mode: "resume" })` or `session_health` to diagnose.'];
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:11:        "negativeHints": ["narrative_delivery", "research_finding"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:18:        "tags": ["runtime", "fix", "search", "behavior"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:20:        "chunk": "The search pipeline now keeps folder discovery as a scoring boost instead of promoting the discovered folder into an exact-match filter, and stage one no longer treats sessionId as a governance scope boundary. Together those changes unblock focused-mode searches that were returning zero candidates. The chunk is about the substantive runtime correction and the precise behavior that changed."
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:45:        "negativeHints": ["narrative_progress", "research_finding"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:54:        "chunk": "Attempt one confirmed that semantic search returned results again, then attempt two kept the work pending until the MCP server restart could happen and the focused-mode fix could be rechecked in order. The implementation compiled before handover, but release was deliberately blocked by the verification gate and only then could the delivery story close. The emphasis is on sequencing, gating, and verification order."
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:79:        "negativeHints": ["research_finding", "narrative_progress"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:95:        "negativeHints": ["research_finding", "narrative_progress"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:103:        "negativeHints": ["narrative_delivery", "research_finding"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:114:        "chunk": "Current state for the continuation: research is complete, the foundation phase is complete, and later phases were dispatched as parallel agents. The blocker is verification of those agent outputs before closure. Next session work is to inspect git diff, review the generated changes, and then finish the remaining template update. The emphasis is the stop-state and resume path, not the command itself."
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:121:        "negativeHints": ["research_finding", "task_update"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:122:        "chunk": "Current state: implementation fixes are compiled, the MCP server was killed to force a clean restart, and runtime verification must happen in a fresh session before the packet can be closed. Active files are the focused handler fix and the stage one and stage two search pipeline modules. The handoff is about what is live right now and what blocks closure."
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:137:        "negativeHints": ["research_finding", "decision"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:141:    "research_finding": [
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:145:        "sourceShape": "research",
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:153:        "sourceShape": "research",
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:154:        "tags": ["architecture", "research", "conclusion", "hybrid"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:156:        "chunk": "The compact code graph work should use a clean-room tree-sitter plus SQLite approach rather than a full graph database. The research across tooling and academic sources points to a hybrid retrieval system: embeddings for recall, structural graph signals for precision, and a compact projection layer for model-facing context. This is a research synthesis chunk."
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:161:        "sourceShape": "research",
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:169:        "sourceShape": "research",
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:231:        "negativeHints": ["research_finding", "handover_state"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:239:        "negativeHints": ["research_finding", "handover_state"],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:258:        "chunk": "Recovery scenarios context loss run resume, state mismatch check git status, memory not found call memory_search, stale context compare timestamps, diagnostic commands list memories, verify file integrity, force re-index. This is generic operator boilerplate repeated across many memory files."
.opencode/skills/system-spec-kit/mcp_server/lib/routing/routing-prototypes.json:265:        "negativeHints": ["metadata_only", "research_finding"],
.opencode/skills/system-spec-kit/mcp_server/tests/constitutional-filtering.vitest.ts:14:vi.mock('../lib/search/vector-index-store.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/constitutional-filtering.vitest.ts:22:  search_weights: {},
.opencode/skills/system-spec-kit/mcp_server/tests/constitutional-filtering.vitest.ts:26:import { getConstitutionalMemories } from '../lib/search/vector-index-queries.js';
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:4:import * as bm25Index from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:582:          content: 'Merged addition that should stay searchable',
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:629:    it('MP5: Attempts immediate BM25 repair and surfaces a warning if repair still fails', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:633:          throw new Error('initial merge BM25 failure');
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:636:          throw new Error('repair merge BM25 failure');
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:650:          104, 'test-spec', '/test/104.md', 'BM25 Repair Existing', 'Original searchable content',
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:662:          title: 'BM25 Repair Existing',
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:663:          content_text: 'Original searchable content',
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:667:          title: 'BM25 Repair Existing',
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:678:        `BM25 repair failed after reconsolidation merge for memory ${result.newMemoryId}: repair merge BM25 failure`,
.opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts:1233:      const errorFn: FindSimilarFn = () => { throw new Error('vector search down'); };
.opencode/skills/system-spec-kit/mcp_server/tools/README.md:3:description: "Typed MCP tool dispatch modules, schema validation, and quick-search delegation."
.opencode/skills/system-spec-kit/mcp_server/tools/README.md:6:  - "memory quick search"
.opencode/skills/system-spec-kit/mcp_server/tools/README.md:28:- `context-tools.ts` - dispatch for `memory_context`.
.opencode/skills/system-spec-kit/mcp_server/tools/README.md:29:- `memory-tools.ts` - dispatch for search, quick search, triggers, save, CRUD, stats, health, validate, and bulk delete.
.opencode/skills/system-spec-kit/mcp_server/tools/README.md:41:- `memory-tools.ts` implements the `memory_quick_search` delegation path by building a richer `memory_search` request and relabeling the returned envelope metadata back to `memory_quick_search`.
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:7:// Learns from user memory selections to improve future search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:8:// Writes to a SEPARATE `learned_triggers` column (NOT FTS5 index).
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:11:// 1. Separate column -- `learned_triggers` TEXT column, NOT in FTS5 index
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:40:/** Selection event recorded when a user selects a search result. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:200: * @param queryTerms - Terms from the user's search query
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:242: * a search result, this function:
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:250: * @param queryId - Unique identifier for the search query
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:252: * @param queryTerms - Terms from the user's search query
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:329:    // Apply learned triggers (Safeguard #1 -- separate column, NOT FTS5)
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:348: * NEVER to the FTS5 index (Safeguard #1).
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:399:    // Do NOT touch memory_fts or any FTS5 table (Safeguard #1).
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:443: * Query learned triggers for search results, applying 0.7x weight.
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts:445: * Searches the learned_triggers column (NOT FTS5) for matches against
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:11:import * as intentClassifier from '../lib/search/intent-classifier.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:13:import { isSessionBoostEnabled, isCausalBoostEnabled, isCommunitySearchFallbackEnabled, isDualRetrievalEnabled, isIntentAutoProfileEnabled } from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:14:import { searchCommunities } from '../lib/search/community-search.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:16:import { executePipeline } from '../lib/search/pipeline/index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:17:import type { PipelineConfig, PipelineResult } from '../lib/search/pipeline/index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:18:import type { IntentWeightsConfig } from '../lib/search/pipeline/types.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:22:import { getStrategyForQuery } from '../lib/search/artifact-routing.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:24:import { collapseAndReassembleChunkResults } from '../lib/search/chunk-reassembly.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:33:} from '../lib/search/search-utils.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:34:// CacheArgsInput used internally by buildCacheArgs (lib/search/search-utils.ts)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:70:} from '../lib/search/session-transition.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:82:} from '../lib/search/progressive-disclosure.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:91:} from '../lib/search/sqlite-fts.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:92:import type { LexicalCapabilitySnapshot } from '../lib/search/sqlite-fts.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:99:} from '../lib/search/session-state.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:102:import type { IntentType, IntentWeights as IntentClassifierWeights } from '../lib/search/intent-classifier.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:104:// RoutingResult, WeightedResult — now used internally by lib/search/search-utils.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:106:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:107:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:109:// Feature catalog: Quality-aware 3-tier search fallback
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:117: * Internal search result row — enriched DB row used within this handler.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:183:  'research',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:288:// ChunkReassemblyResult — now imported from lib/search/chunk-reassembly.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:330:  includeArchived?: boolean; // REQ-206: include archived memories in search (default false)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:338:  /** REQ-D5-003: Presentation profile ('quick'|'research'|'resume'|'debug'). Default: full response. */
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:344:// resolveRowContextType — now imported from lib/search/search-utils.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:372:    console.warn('[memory-search] Failed to attach telemetry payload:', message);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:467:    tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:559:// resolveArtifactRoutingQuery, applyArtifactRouting — now imported from lib/search/search-utils.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:560:// CacheArgsInput — now imported from lib/search/search-utils.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:561:// parseNullableInt, collapseAndReassembleChunkResults — now imported from lib/search/chunk-reassembly.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:609:/** Handle memory_search tool — performs hybrid vector/BM25 search with intent-aware ranking.
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:611: * @returns MCP response with ranked search results
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:614:  const _searchStartTime = Date.now();
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:668:  // Validate at least one search input is provided (moved from schema superRefine for GPT compatibility)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:680:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:685:          hint: 'Retry the original search to generate a fresh continuation cursor',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:692:      tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:699:      startTime: _searchStartTime,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:720:          tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:739:      tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:751:      tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:772:  } catch (_error: unknown) { /* eval logging must never break search */ }
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:791:      console.warn(`[memory-search] Invalid intent '${explicitIntent}', using auto-detection`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:802:      console.error(`[memory-search] Intent auto-detected as '${detectedIntent}' (fallback: ${classification.reason})`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:804:      console.error(`[memory-search] Intent auto-detected as '${detectedIntent}' (confidence: ${intentConfidence.toFixed(2)})`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:811:    console.error(`[memory-search] Intent confidence ${intentConfidence.toFixed(3)} below floor ${INTENT_CONFIDENCE_FLOOR}, overriding '${detectedIntent}' → 'understand'`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:825:        console.error(`[memory-search] Intent-to-profile auto-routing: '${detectedIntent}' → profile '${autoProfile}'`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:828:      // Auto-profile is best-effort — never breaks search
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:849:  // the affected memory_search entries on the next lookup. We deliberately
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:891:  const cacheKey = toolCache.generateCacheKey('memory_search', cacheArgs);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:901:    responseToReturn = buildSearchResponseFromPayload(cachedPayload, _searchStartTime, true);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:915:      searchType: (hasValidConcepts && concepts!.length >= 2)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:917:        : 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:952:    // Phase B T018/T019: Community search fallback — inject community members on weak results
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:966:          const communityResults = searchCommunities(effectiveQuery, requireDb(), 5);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:998:          console.warn(`[memory-search] Community search fallback failed (fail-open): ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1057:        `[memory-search] Lexical capability path '${lexicalCapability.lexicalPath}' (fallbackState: ${lexicalCapability.fallbackState})`
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1156:      pipelineConfig.searchType,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1201:      toolCache.set(cacheKey, cachePayload, { toolName: 'memory_search' });
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1205:      ? buildSearchResponseFromPayload(cachePayload, _searchStartTime, false)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1236:        console.warn('[memory-search] Failed to parse cached response for dedup:', message);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1252:      console.warn('[memory-search] Cached response shape mismatch: missing "data" object, skipping dedup');
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1254:      console.warn('[memory-search] Cached response shape mismatch: "data.results" is not an array, skipping dedup');
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1343:  // Consumption instrumentation — log search event (fail-safe, never throws)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1360:        event_type: 'search',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1366:        latency_ms: Date.now() - _searchStartTime,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1370:  } catch (_error: unknown) { /* instrumentation must never cause search to fail */ }
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1392:        latencyMs: Date.now() - _searchStartTime,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1406:  } catch (_error: unknown) { /* eval logging must never break search */ }
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1408:  // REQ-D4-001: Implicit feedback — log search_shown events for returned results
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1425:          const queryId = _evalQueryId ? String(_evalQueryId) : String(_searchStartTime);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1427:            type: 'search_shown',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1431:            timestamp: _searchStartTime,
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1438:  } catch (_error: unknown) { /* feedback logging must never break search */ }
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1440:  // REQ-014: Query flow tracking + result_cited for includeContent searches
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1467:        const queryId = _evalQueryId ? String(_evalQueryId) : String(_searchStartTime);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1474:        // Log result_cited for includeContent searches (content was embedded = cited)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1480:  } catch (_error: unknown) { /* query flow tracking must never break search */ }
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1496:        // Profile formatting is best-effort — never breaks search
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1531:const handle_memory_search = handleMemorySearch;
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:1534:  handle_memory_search,
.opencode/skills/system-spec-kit/mcp_server/lib/graph/usage-ranking-signal.ts:8:import { isUsageRankingEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints.vitest.ts:7:import * as vectorIndexMod from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints.vitest.ts:8:import * as bm25IndexMod from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints.vitest.ts:597:        VALUES (?, 'search', ?, 1, ?)
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/composite-scoring.ts:23: * fallbacks, search-enriched properties like similarity, etc.).
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/composite-scoring.ts:198:  research: 2.0,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/composite-scoring.ts:483:      'research': ['research', 'investigate', 'analysis', 'findings', 'experiment'],
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:27:  'research_finding',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:38:  'research',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:57:type PacketKind = 'feature' | 'phase' | 'remediation' | 'research' | 'unknown';
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:128:  structuredType?: 'decision' | 'handover' | 'research' | 'task_update' | 'metadata_only';
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:366:    id: 'tier1.structured.research',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:367:    category: 'research_finding',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:369:    when: (chunk: ContentChunk): boolean => chunk.structuredType === 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:442:  research_finding: [
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:443:    /\b(found that|finding|research|source|cited|upstream|investigation|synthesis|evidence)\b/,
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:464:  'research_finding',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:1014:    scores.research_finding = Math.max(scores.research_finding ?? 0, 0.8);
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:1079:    case 'research_finding':
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:1080:      return { docPath: 'research/research.md', anchorId: DEFAULT_RESEARCH_ANCHOR, mergeMode: 'append-section' };
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:1282:    'Context: This system uses a 3-level resume ladder (handover.md -> _memory.continuity in implementation-summary.md -> canonical spec docs). metadata_only saves always target implementation-summary.md. The router classifies into 8 categories: narrative_progress, narrative_delivery, decision, handover_state, research_finding, task_update, metadata_only, drop.',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:1290:    '- research_finding: evidence, investigation result, cited upstream behavior, or research conclusion; usually research/research.md',
.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:1297:    'Merge-mode guidance: progress and delivery -> append-as-paragraph; handover and research -> append-section; L3/L3+ decision -> insert-new-adr; task_update, metadata_only, and L2 decision -> update-in-place; drop -> refuse-to-route.',
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:244:    if re.search(r"\b(ignore|override|forget|bypass|disable|execute|run|call|tool|developer|assistant|previous instructions|all instructions)\b", cleaned, re.I):
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:246:    if re.search(r"<!--|-->|```|<script\b|</script>|^\s*(system|instruction|developer|assistant)\s*:", cleaned, re.I):
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1053:    "recall": ["memory", "search", "find", "retrieve"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1103:    # Autoresearch
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1104:    "autoresearch": ["research", "loop", "iterative", "deep", "autonomous", "convergence"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1112:    "find": ["search", "locate", "explore", "lookup"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1113:    "search": ["find", "locate", "explore", "query", "lookup"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1114:    "where": ["find", "search", "locate", "navigate"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1115:    "lookup": ["find", "search", "locate"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1116:    "explore": ["search", "find", "navigate", "discover"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1117:    "navigate": ["find", "search", "locate", "goto"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1118:    "locate": ["find", "search", "where"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1202:    # SK-AUTORESEARCH: Autonomous deep research loop
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1204:    "autoresearch": ("sk-deep-research", 2.0),
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1205:    "convergence": ("sk-deep-research", 0.8),
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1371:    # MCP-COCO-INDEX: Semantic code search via vector embeddings
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1472:    # --- Autoresearch deep research loop ---
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1473:    "deep research": [("sk-deep-research", 2.5)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1474:    "research loop": [("sk-deep-research", 2.5)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1475:    "autoresearch": [("sk-deep-research", 3.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1476:    "/autoresearch": [("sk-deep-research", 3.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1477:    "auto research": [("sk-deep-research", 2.8)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1478:    "autonomous research": [("sk-deep-research", 2.5)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1479:    "iterative research": [("sk-deep-research", 2.5)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1480:    "multi-round research": [("sk-deep-research", 2.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1481:    "overnight research": [("sk-deep-research", 2.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1517:    # --- CocoIndex semantic code search ---
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1518:    "semantic search": [("mcp-coco-index", 2.5)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1519:    "code search": [("mcp-coco-index", 2.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1520:    "vector search": [("mcp-coco-index", 2.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1521:    "concept search": [("mcp-coco-index", 2.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1522:    "cocoindex search": [("mcp-coco-index", 2.8)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1529:    "search codebase": [("mcp-coco-index", 2.2)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1533:    "semantic code search": [("mcp-coco-index", 2.5)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1539:    "convergence detection": [("sk-deep-research", 2.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1571:    "google search grounding": [("cli-gemini", 2.0)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1652:    # at `kind_priority=2`, so `/spec_kit:deep-research` lost its owning-skill
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1653:    # signal (should route to `sk-deep-research`, not `command-spec-kit`).
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1657:    # Execution-mode suffixes (:auto, :confirm, :with-phases, :with-research)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1675:    "command-spec-kit-deep-research": {
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1676:        "description": "Run the autonomous deep-research loop using /spec_kit:deep-research.",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1677:        "slash_markers": ["/spec_kit:deep-research", "spec_kit:deep-research"],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1678:        "owning_skill": "sk-deep-research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1740:    "command-spec-kit-deep-research": "sk-deep-research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1789:# Multiplier applied to CocoIndex relevance score (0-1) to produce an advisor boost.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1796:# Subprocess timeout for built-in ccc search (seconds).
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1799:# Max results from CocoIndex when using built-in search.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1804:    "search the codebase",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1805:    "search the code base",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1806:    "search semantically",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1838:    "search",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1905:    """Split text into normalized search terms while filtering stop words."""
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1927:    return pattern.search(text) is not None
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1981:    """Map a CocoIndex result file path to a known skill name.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:1986:    match = _SKILL_PATH_RE.search(file_path)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2004:def _cocoindex_search_builtin(
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2009:    """Run semantic search via ``ccc search`` and return parsed hits.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2026:            [ccc_bin, "search", query, "--limit", str(limit * 2)],
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2047:    """Extract skill references from ``ccc search`` text output.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2073:            skill_match = _SKILL_PATH_RE.search(file_path)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2100:    """Blend CocoIndex semantic search results into keyword scoring.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2124:    """Return the preferred CocoIndex binary path, favoring the repo-local install."""
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2130:def built_in_semantic_search_disabled() -> bool:
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2131:    """Return True when external CocoIndex lookup is disabled via environment."""
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2137:    """Return True when the prompt is explicitly asking for exact-text search."""
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2144:def should_auto_use_semantic_search(prompt: str) -> bool:
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2145:    """Decide whether semantic search should run automatically for this prompt."""
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2534:# Iteration-loop phrases that imply skill-owned workflow (deep-research / deep-review)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2538:    "deep-research", "deep research", "deep-review", "deep review",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2539:    "autoresearch", "auto research", "research loop", "review loop",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2540:    "iterative research", "iterative review", "autonomous research", "autonomous review",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2542:    "/spec_kit:deep-research", "/spec_kit:deep-review",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2543:    "spec_kit:deep-research", "spec_kit:deep-review",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2546:# T-SAP-02 (R45-002): Deep-research disambiguation phrases. When the prompt
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2547:# contains one of these and both `sk-deep-research` and `sk-code-review`
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2549:# so `sk-deep-research` keeps the primary slot. Wording-sensitive audit/review
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2550:# tokens must not steal a deep-research prompt back into the generic review
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2553:    "deep research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2554:    "deep-research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2555:    "autoresearch",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2556:    "/autoresearch",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2557:    "research loop",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2558:    "iterative research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2559:    "autonomous research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2560:    "auto research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2561:    "/spec_kit:deep-research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2562:    "spec_kit:deep-research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2584:def _apply_deep_research_disambiguation(
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2588:    """Ensure sk-deep-research beats sk-code-review by ≥ 0.10 on deep-research prompts.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2590:    T-SAP-02 (R45-002): audit/review-token overlap between deep-research prompts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2592:    contains an unambiguous deep-research marker AND both `sk-deep-research`
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2594:    ``DISAMBIGUATION_MARGIN`` so the router returns a stable deep-research
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2629:        winner = _find("sk-deep-research")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2632:            _enforce_margin(winner, loser, "sk-deep-research")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2647:    Background: when a user asks to run iterations of deep-research or deep-review with
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2694:        semantic_hits: Optional CocoIndex search results as a list of
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2707:    # are important signals for semantic search but would otherwise be filtered
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2718:    if should_auto_use_semantic_search(prompt):
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2720:        boost_reasons.setdefault("mcp-coco-index", []).append("!intent:semantic-code-search")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2722:    # Blend CocoIndex semantic search results when available
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2793:    search_terms = expand_query(tokens) if tokens else []
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2803:        for term in search_terms:
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2864:    # T-SAP-02 (R45-002): disambiguate deep-research vs code-review and
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:2867:    _apply_deep_research_disambiguation(recommendations, prompt_lower)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3093:        if semantic_mode and not built_in_semantic_search_disabled():
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3094:            hits = _cocoindex_search_builtin(trimmed, REPO_ROOT)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3095:        elif should_auto_use_semantic_search(trimmed) and not built_in_semantic_search_disabled():
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3096:            hits = _cocoindex_search_builtin(trimmed, REPO_ROOT)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3144:  # CocoIndex semantic search (built-in, requires ccc daemon):
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3148:  # CocoIndex semantic search (pre-computed MCP results):
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3182:                         help='Run CocoIndex semantic search (via ccc CLI) to supplement keyword matching.')
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3184:                         help='Pre-computed CocoIndex results as JSON array of {"path": str, "score": float} objects.')
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3210:    # Parse pre-computed semantic hits (JSON array from MCP search results)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3291:    # Resolve semantic hits: pre-computed > built-in search > none
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3293:    if semantic_hits is None and args.semantic and not built_in_semantic_search_disabled():
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3294:        semantic_hits = _cocoindex_search_builtin(args.prompt, REPO_ROOT)
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3295:    elif semantic_hits is None and should_auto_use_semantic_search(args.prompt) and not built_in_semantic_search_disabled():
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_advisor.py:3296:        semantic_hits = _cocoindex_search_builtin(args.prompt, REPO_ROOT)
.opencode/skills/system-spec-kit/mcp_server/tests/memory-delete-cascade.vitest.ts:7:type VectorIndexModule = typeof import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-delete-cascade.vitest.ts:18:    mod = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:4:// Dispatch for L2-L4 memory tools: search, triggers, save,
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:62:  'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:63:  'memory_quick_search',
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:64:  'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:78:    case 'memory_search':         return handleMemorySearch(parseArgs<SearchArgs>(validateToolArgs('memory_search', args)));
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:79:    case 'memory_quick_search': {
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:80:      // E3: Delegate to memory_search with sensible defaults
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:81:      const validated = validateToolArgs('memory_quick_search', args);
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:96:      return relabelResponseTool(response, 'memory_quick_search');
.opencode/skills/system-spec-kit/mcp_server/tools/memory-tools.ts:98:    case 'memory_match_triggers': return handleMemoryMatchTriggers(parseArgs<TriggerArgs>(validateToolArgs('memory_match_triggers', args)));
.opencode/skills/system-spec-kit/mcp_server/lib/graph/community-summaries.ts:7:import { isCommunitySummariesEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-fallback-fingerprint.vitest.ts:243:  vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-fallback-fingerprint.vitest.ts:244:    const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-fallback-fingerprint.vitest.ts:251:  vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-fallback-fingerprint.vitest.ts:252:    const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-fallback-fingerprint.vitest.ts:398:    vi.doUnmock('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-fallback-fingerprint.vitest.ts:399:    vi.doUnmock('../lib/search/search-flags.js');
.opencode/skills/system-spec-kit/mcp_server/handlers/causal-graph.ts:10:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:11:  searchBoost: number;
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:35:    searchBoost: 3.0,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:44:    searchBoost: 2.0,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:51:    searchBoost: 1.5,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:58:    searchBoost: 1.0,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:65:    searchBoost: 0.5,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:72:    searchBoost: 0.0,
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:76:    description: 'Hidden from search results',
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:95:// Apply tier boost to a search score (critical=2x, important=1.5x, etc.)
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:101:  return score * config.searchBoost;
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:104:// Check if tier should be excluded from search (deprecated tier)
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:147:// SQL WHERE clause for searchable tiers (excludes deprecated)
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:152:// Check if tier should always surface in search (constitutional)
.opencode/skills/system-spec-kit/mcp_server/lib/scoring/importance-tiers.ts:222:    research: 'normal',
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-relevance.ts:38: * Compute FolderScore for each spec folder from grouped search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-relevance.ts:47: * @param results  - Array of scored search results
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-relevance.ts:134: * Enrich search results with folder-level relevance metadata.
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-relevance.ts:144: * @param results      - Original scored search results
.opencode/skills/system-spec-kit/mcp_server/tests/p0-c-graph-metadata-laundering.vitest.ts:14:import { __testables as stage1Testables } from '../lib/search/pipeline/stage1-candidate-gen.js';
.opencode/skills/system-spec-kit/mcp_server/lib/graph/temporal-edges.ts:10:import { isTemporalEdgesEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:25:} from '../lib/search/query-surrogates';
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:60:    summary: overrides?.summary ?? 'A module that fuses ranking signals from multiple search channels.',
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:150:    const content = 'The system aka "Memory Engine" provides search capabilities.';
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:330:      ['How to configure search'],
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:333:    expect(questions.some((q) => q.includes('How do I configure search'))).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:483:      surrogateQuestions: ['How do I configure search pipelines?'],
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:485:    const result = matchSurrogates('configure search pipelines', surrogates);
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:492:      summary: 'A comprehensive guide to vector embedding search techniques.',
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:494:    const result = matchSurrogates('vector embedding search', surrogates);
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts:777:The search pipeline uses Reciprocal Rank Fusion (RRF) to combine results.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:9:// When a user selects a memory from search results, that selection
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:28:  /** The search mode used (e.g. "search", "context", "trigger"). */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:29:  searchMode?: string;
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:125:    search_mode TEXT,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:214: * Record a user's selection of a memory from search results.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:237:        (query_id, memory_id, search_mode, intent, selected_rank,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:243:      selectionContext.searchMode ?? null,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:280:      SELECT id, query_id, memory_id, search_mode, intent,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:291:      search_mode: string | null;
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-feedback.ts:305:        searchMode: row.search_mode ?? undefined,
.opencode/skills/system-spec-kit/mcp_server/lib/ops/README.md:76:- `mcp_server/lib/search/` - Search modules that consume the indexed data produced by these operations.
.opencode/skills/system-spec-kit/mcp_server/tests/trigger-matcher.vitest.ts:36:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:3:import type { PipelineRow, Stage2Input } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:4:import { formatSearchResults, type MemoryResultEnvelope } from '../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:5:import { executeStage2 } from '../lib/search/pipeline/stage2-fusion';
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:46:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:57:vi.mock('../lib/search/graph-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:61:vi.mock('../lib/search/session-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:65:vi.mock('../lib/search/causal-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:87:vi.mock('../lib/search/learned-feedback', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:96:vi.mock('../lib/search/anchor-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:100:vi.mock('../lib/search/validation-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:104:vi.mock('../lib/search/pipeline/stage2b-enrichment', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:124:vi.mock('../lib/search/graph-calibration', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:131:vi.mock('../lib/search/pipeline/ranking-contract', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:153:vi.mock('../lib/search/session-transition', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/provenance-envelope.vitest.ts:157:vi.mock('../lib/search/recovery-payload', () => ({
.opee/skill/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:167:     Group 3: hybridSearchEnhanced — graph channel bypass
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:170:  describe('T022-2e: hybridSearchEnhanced — graph search fn NOT called when graphFn is null', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:183:    it('T022-2e-null: hybridSearchEnhanced with null graphFn — spy never called', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:187:      await hybridSearchEnhanced('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:192:    it('T022-2e-wired: hybridSearchEnhanced with real graphFn — spy called when useGraph=true', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:193:      // Positive control for hybridSearchEnhanced code path
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:197:      await hybridSearchEnhanced('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:199:      // HybridSearchEnhanced may fall through to hybridSearch internally;
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:204:    it('T022-2e-off: hybridSearchEnhanced with real graphFn — spy NOT called when useGraph=false', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:208:      await hybridSearchEnhanced('test query', null, { useGraph: false });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:245:      // Drive some counters via hybridSearchEnhanced with a wired graphFn
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:258:      await hybridSearchEnhanced('probe query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:260:      // At least totalQueries should be non-zero after a search with a wired graphFn
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts:327:      const results = await hybridSearch('probe query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/lib/eval/edge-density.ts:211:    '  neutralising its contribution to hybrid search until R10 is complete.',
.opencode/skills/system-spec-kit/mcp_server/lib/governance/scope-governance.ts:8:import { ensureGovernanceTables } from '../search/vector-index-schema.js';
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:141:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:198:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:240:    vi.doMock('../lib/search/vector-index', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:241:      const actual = await importOriginal<typeof import('../lib/search/vector-index')>();
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:264:      vi.doUnmock('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:274:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:317:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:365:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:410:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:442:    const tempDir = makeTempDir('spec-kit-search-reassembly-');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:447:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-010-index-large-files.vitest.ts:450:    const memorySearch = await import('../handlers/memory-search');
.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:250:  it('T020-02: Generates memory_search command with sessionId when specFolder is not provided', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/continue-session.vitest.ts:254:  it('T020-03: Generates generic memory_search when neither specFolder nor sessionId is provided', () => {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/README.md:31:- BM25 baselines, ablations, k-sensitivity, and state baselines.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/README.md:42:| `bm25-baseline.ts` | BM25-only baseline measurement and baseline metric persistence |
.opencode/skills/system-spec-kit/mcp_server/lib/eval/README.md:72:- `../search/README.md`
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/query.ts:51:    if (args.loopType !== 'research' && args.loopType !== 'review') {
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/query.ts:52:      return errorResponse('loopType must be "research" or "review"');
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/query.ts:68:	        if (args.loopType !== 'research') {
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/query.ts:69:	          return errorResponse('uncovered_questions is only valid for research graphs; use coverage_gaps for review graphs');
.opencode/skills/system-spec-kit/mcp_server/lib/resume/resume-ladder.ts:83:  'research.md',
.opencode/skills/system-spec-kit/mcp_server/lib/search/confidence-truncation.ts:5:import { isConfidenceTruncationEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/database/README.md:3:description: "Runtime SQLite storage for memory, structural code graph, vectors, FTS, and coordination files."
.opencode/skills/system-spec-kit/mcp_server/database/README.md:73:- Structural reads (`code_graph_query`, `code_graph_context`) can perform bounded inline selective refresh against `code-graph.sqlite` when the stale set is small enough.
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-index.vitest.ts:107:    '../lib/search/search-flags.js',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-index.vitest.ts:264:  vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-index.vitest.ts:265:    const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/crash-recovery.vitest.ts:506:        specFolder: 'specs/022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/crash-recovery.vitest.ts:519:      expect(content).toContain('/spec_kit:resume specs/022-hybrid-rag-fusion');
.opencode/skills/system-spec-kit/mcp_server/lib/eval/memory-state-baseline.ts:136:    "SELECT COUNT(*) AS value FROM memory_index WHERE context_type IS NULL OR TRIM(context_type) = '' OR context_type NOT IN ('research','implementation','planning','general','decision','discovery')",
.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:47:      (101, 'system-spec-kit/020-mcp-working-memory-hybrid-rag', '/tmp/spec.md', 'Spec', 'important', '[]', CURRENT_TIMESTAMP),
.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:48:      (102, 'system-spec-kit/020-mcp-working-memory-hybrid-rag', '/tmp/error.log', 'Errors', 'normal', '[]', CURRENT_TIMESTAMP)
.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:133:    expect(matchRule('memory_search', 'spec.md error context')).not.toBeNull();
.opencode/skills/system-spec-kit/mcp_server/tests/extraction-adapter.vitest.ts:134:    expect(matchRule('memory_context', 'spec.md metadata')).not.toBeNull();
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:5:      "query": "what does maxTriggersPerMemory control in the search pipeline",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:10:      "expectedResultDescription": "Memory or spec covering search-weights.json and the MAX_TRIGGERS_PER_MEMORY constant in vector-index-impl.ts. Should surface the T000c audit or related sprint-0 documentation.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:25:      "query": "how does intent classification affect search result ranking",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:30:      "expectedResultDescription": "Should surface memories about adaptive-fusion.ts (7 intent profiles), intent-classifier.ts, and memory_context intent routing. Cross-document because the behavior spans multiple modules.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:35:      "query": "what decisions led to using RRF instead of a weighted linear combination for search fusion",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:40:      "expectedResultDescription": "Decision records from hybrid-rag-fusion spec (spec 139) about fusion strategy selection. Should surface rationale for RRF over linear weighted sum.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:50:      "expectedResultDescription": "Should surface adaptive-fusion.ts (FEATURE_FLAG constant, isFeatureEnabled check), search-flags.ts, and rollout-policy.ts. Tests understanding the opt-out semantics.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:85:      "query": "memory_context returns wrong results when token pressure is high",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:115:      "query": "which spec documents were added during the hybrid RAG fusion sprint",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:120:      "expectedResultDescription": "Should surface memories in spec folder system-spec-kit/022-hybrid-rag-fusion (89 memories) and 140-hybrid-rag-fusion-refinement. Lists spec documents created in those sprints.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:135:      "query": "smartRanking config weights in search-weights.json are inconsistent with the code fallback values",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:155:      "query": "what was decided about removing the cross-encoder configuration from search-weights.json",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:251:      "notes": "From T007b Pattern 3: feature description passed to memory_context before implementation."
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:275:      "query": "adaptive fusion search pipeline architecture",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:280:      "expectedResultDescription": "Deep investigation query. Should surface adaptive-fusion.ts, hybrid-search.ts, rrf-fusion.ts, and related spec memories spanning the search stack.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:285:      "query": "how does the @context agent coordinate sub-agent search strategies",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:295:      "query": "list all memories in the hybrid RAG fusion spec folder",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:300:      "expectedResultDescription": "Spec-scoped browse. Should surface memory titles and tiers from spec folder system-spec-kit/022-hybrid-rag-fusion or 140-hybrid-rag-fusion-refinement.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:330:      "expectedResultDescription": "AND-search style query. Should surface causal-edges.ts, memory_causal_link tool schema, and any memories about the causal graph design.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:331:      "notes": "From T007b Pattern 8: concept AND search for 'causal edges' AND 'decision lineage'."
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:365:      "query": "SPECKIT_BM25 environment variable controls what behavior",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:370:      "expectedResultDescription": "Should surface bm25-index.ts isBm25Enabled() function and any documentation about the BM25 feature flag.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:415:      "query": "the memory_search tool returns stale results after index rebuild",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:425:      "query": "what is the difference between memory_context and memory_search for context retrieval",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:430:      "expectedResultDescription": "Should surface both memory_context (L1 unified entry) and memory_search (L2 core) tool schemas and any documentation comparing their use cases.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:450:      "expectedResultDescription": "Should surface causal-boost.ts, search-flags.ts, and any spec memory that introduced SPECKIT_CAUSAL_BOOST.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:455:      "query": "how does RRF fusion combine vector and BM25 channel scores",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:515:      "query": "find the decision that established the WARM tier as the minimum search state",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:521:      "notes": "Decision tracing for a specific default value in the search configuration."
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:611:      "notes": "Derived from \"reciprocal rank fusion\" trigger phrase in the hybrid search documentation."
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:655:      "query": "BM25 tokenization stemming",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:661:      "notes": "Derived from \"BM25\" and \"stemming\" trigger phrases in the BM25 index module."
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:690:      "expectedResultDescription": "Should surface mmr-reranker.ts and any spec memories about diversity-aware reranking in the search pipeline.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:725:      "query": "when should I use memory_search versus memory_context",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:770:      "expectedResultDescription": "Should surface decision records or spec memories explaining the choice of SQLite + FTS5 + custom vector storage over alternatives like Pinecone or Chroma.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:820:      "expectedResultDescription": "Should surface graph-search-fn.ts, causal-edges.ts, and the T000a baseline note about graphHitRate=0 being expected until the graph is populated.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:825:      "query": "why is my new memory not appearing in search results after saving",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:831:      "notes": "Manual bug query about indexing lag — realistic user confusion about save vs. search consistency."
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:855:      "query": "I want to add telemetry tracking to the hybrid search pipeline",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:905:      "query": "show me the checklist for the sprint 0 hybrid RAG fusion refinement",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:915:      "query": "is there a research document for the hybrid RAG fusion approach",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:920:      "expectedResultDescription": "Should surface research/research.md from the 139-hybrid-rag-fusion or 140-hybrid-rag-fusion-refinement spec folder if it exists.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:925:      "query": "what is the task breakdown for the T008 BM25 baseline measurement task",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:941:      "notes": "Manual search for a specific document type about a completed implementation."
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:955:      "query": "can the trigger matching and vector search be unified into a single query path",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:960:      "expectedResultDescription": "Should surface trigger-matcher.ts, vector-index.ts, hybrid-search.ts, and any architectural decision about keeping the two paths separate.",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:1005:      "query": "can the eval logging system be used to exfiltrate search query content",
.opencode/skills/system-spec-kit/mcp_server/lib/eval/data/ground-truth.json:1045:      "query": "SQL injection prevention in the memory search query parameter",
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:4:import * as searchHandlerModule from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:37:      expect(searchHandlerModule).toBeDefined();
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:94:      if (searchHandlerModule?.handleMemorySearch) {
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:96:          name: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:97:          run: () => searchHandlerModule.handleMemorySearch({} as Parameters<typeof searchHandlerModule.handleMemorySearch>[0]),
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:140:          const isStructuredSearchError = h.name === 'search' && hasStructuredContentError(result);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:162:      if (!searchHandlerModule?.handleMemorySearch) return;
.opencode/skills/system-spec-kit/mcp_server/tests/integration-error-recovery.vitest.ts:166:        const result = await searchHandlerModule.handleMemorySearch({ query: 12345 });
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/README.md:3:description: "MCP handlers for deep-loop research and review coverage graphs."
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/README.md:20:- `convergence.ts` - computes stop/continue guidance for research and review loops.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-types.ts:8:/** Supported embedding input shapes for vector search and mutation operations. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-types.ts:75:/** Represents a vector-search memory row shared by query and store helpers. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-types.ts:132:/** Controls vector search filtering and ranking behavior. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-types.ts:144:/** Represents an enriched search result returned to callers. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-types.ts:162:  searchMethod?: string;
.opencode/skills/system-spec-kit/mcp_server/tests/typed-traversal.vitest.ts:8:import * as causalBoost from '../lib/search/causal-boost';
.opencode/skills/system-spec-kit/mcp_server/tests/typed-traversal.vitest.ts:9:import type { RankedSearchResult } from '../lib/search/causal-boost';
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-generator.ts:101: * FTS5-based matching (scripts/map-ground-truth-ids.ts).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-generator.ts:108:  // The production memory_fts index using multi-strategy FTS5 search.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ground-truth-generator.ts:292:    ? `ALL ${gates.length} diversity gates PASSED. Dataset ready for T008 BM25 baseline measurement.`
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:319:<!-- Keywords: autoresearch, packet anchor -->
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:327:            if {"autoresearch", "packet anchor"}.issubset(keyword_variants):
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:492:    # T243-SA-011: T-SAP-02 / R45-002 deep-research vs sk-code-review margin >= 0.10
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:495:            "deep research audit this subsystem",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:496:            "autoresearch review the architecture",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:497:            "research loop review architecture findings",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:509:            dr = by_skill.get("sk-deep-research")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:518:            ok("T243-SA-011: deep-research disambiguation enforces >= 0.10 margin")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:521:                "T243-SA-011: deep-research disambiguation enforces >= 0.10 margin",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:525:        fail_test("T243-SA-011: deep-research disambiguation enforces >= 0.10 margin", str(exc))
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:710:    # T243-SA-016: T-TEST-NEW-09 / R46-001 — `/spec_kit:deep-research` must route
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:711:    # to `sk-deep-research`, NOT collapse to the generic `command-spec-kit`. The
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:717:        # includes the slash marker. Both must prefer sk-deep-research.
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:719:            "/spec_kit:deep-research",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:720:            "run /spec_kit:deep-research on packet 016",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:721:            "kick off /spec_kit:deep-research :auto for the foundational runtime",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:731:            dr = by_skill.get("sk-deep-research")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:733:            # sk-deep-research MUST be present as a recommendation. command-spec-kit
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:734:            # may also appear, but sk-deep-research must rank at least as high
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:735:            # (higher confidence OR equal with sk-deep-research listed first).
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:737:                failures.append(f"{prompt!r}: sk-deep-research missing from recs")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:743:                    failures.append(f"{prompt!r}: sk-deep-research={dr_conf:.2f} < command-spec-kit={cmd_conf:.2f}")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:745:            ok("T243-SA-016: /spec_kit:deep-research routes to sk-deep-research (not command-spec-kit)")
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:748:                "T243-SA-016: /spec_kit:deep-research routes to sk-deep-research (not command-spec-kit)",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:753:            "T243-SA-016: /spec_kit:deep-research routes to sk-deep-research (not command-spec-kit)",
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/python/test_skill_advisor.py:763:            ("run /spec_kit:deep-research :auto on this packet", "sk-deep-research"),
.opencode/skills/system-spec-kit/mcp_server/tests/cross-encoder-circuit-breaker.vitest.ts:9:import { __testables } from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:6:} from '../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:51:    spec_folder: 'specs/system-spec-kit/022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:69:    'hybrid',
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/upsert.ts:50:  return loopType === 'research' || loopType === 'review';
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/upsert.ts:75:      return errorResponse('loopType must be "research" or "review"');
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/README.md:13:`lib/coverage-graph/` owns the dedicated deep-loop graph store used by research and review loops.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-flags.ts:12:} from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-flags.ts:25: * ladder defined in `search-flags.ts`.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:4:// Feature catalog: BM25-only baseline
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:6:// Runs the ground truth query set through the BM25/FTS5-only
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:11:// Keyword search achieves without any semantic, graph, or trigger
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:15://   - The search function is injected as a dependency so tests
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:40:/** Configuration options for the BM25 baseline runner. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:41:export interface BM25BaselineConfig {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:50:/** Metrics produced by a single BM25 baseline run. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:51:export interface BM25BaselineMetrics {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:60:/** Full result returned by runBM25Baseline(). */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:61:export interface BM25BaselineResult {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:62:  metrics: BM25BaselineMetrics;
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:85:  hybridMRR?: number;
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:86:  /** BM25/hybrid ratio (relative mode only). */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:91: * A single search result as returned by the injected BM25 search function.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:92: * Mirrors the shape used in hybrid-search.ts so callers can reuse the same
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:95:export interface BM25SearchResult {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:98:  /** Retrieval score (raw BM25 / FTS5 rank). */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:106: * Used to evaluate results returned by the injected search function.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:115: * Injected BM25-only search function signature.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:118: * using ONLY the BM25/FTS5 channel (vector, graph, trigger disabled).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:119: * For production use, wire up the FTS5 path from hybrid-search with all
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:122:export type BM25SearchFn = (
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:125:) => BM25SearchResult[] | Promise<BM25SearchResult[]>;
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:132: * Evaluate the BM25 MRR@5 value against the contingency decision matrix.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:136: *     BM25 alone is very strong — semantic/graph additions may not
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:141: *     BM25 is moderate — semantic/graph channels must demonstrably
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:146: *     BM25 alone is weak — strong justification for multi-channel
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:147: *     retrieval. Proceed with hybrid search implementation.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:160:        'BM25 alone is very strong — semantic/graph additions may not justify complexity. ' +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:163:        'search is worth the operational overhead.',
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:174:        'BM25 is moderate — semantic/graph channels should demonstrably improve over this baseline. ' +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:186:      'BM25 alone is weak — strong justification for multi-channel retrieval. ' +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:188:      'adds meaningful value. Proceed with hybrid search implementation.',
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:194:   Compares BM25 MRR@5 as a percentage of hybrid MRR@5.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:195:   Spec: "BM25 >= 80% of hybrid MRR@5" → PAUSE.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:199: * Evaluate BM25 performance relative to hybrid MRR@5 (spec-compliant).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:202: *   ratio = bm25MRR / hybridMRR
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:205: *     BM25 achieves ≥80% of hybrid — multi-channel adds little value.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:208: *     BM25 achieves 50-79% of hybrid — channels need per-channel evidence.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:211: *     BM25 achieves <50% of hybrid — multi-channel clearly justified.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:213: * @param bm25MRR   - BM25-only MRR@5 (must be in [0, 1]).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:214: * @param hybridMRR - Hybrid/multi-channel MRR@5 (must be in (0, 1]).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:219:  hybridMRR: number,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:221:  if (!Number.isFinite(bm25MRR) || !Number.isFinite(hybridMRR) || hybridMRR <= 0) {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:224:      hybridMRR,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:230:        'Hybrid/BM25 MRR@5 is non-finite, zero, or negative — cannot compute meaningful ratio. ' +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:231:        'Defaulting to PROCEED until hybrid baseline is established.',
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:235:  const ratio = bm25MRR / hybridMRR;
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:240:      hybridMRR,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:246:        `BM25 achieves ${(ratio * 100).toFixed(1)}% of hybrid MRR@5 ` +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:247:        `(${bm25MRR.toFixed(4)} / ${hybridMRR.toFixed(4)}). ` +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:248:        'The multi-channel architecture adds marginal value over keyword search alone. ' +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:256:      hybridMRR,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:262:        `BM25 achieves ${(ratio * 100).toFixed(1)}% of hybrid MRR@5 ` +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:263:        `(${bm25MRR.toFixed(4)} / ${hybridMRR.toFixed(4)}). ` +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:271:    hybridMRR,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:277:      `BM25 achieves only ${(ratio * 100).toFixed(1)}% of hybrid MRR@5 ` +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:278:      `(${bm25MRR.toFixed(4)} / ${hybridMRR.toFixed(4)}). ` +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:279:      'Multi-channel retrieval provides substantial improvement over keyword search. ' +
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:280:      'Proceed with hybrid search optimization.',
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:414: * Record BM25 baseline metrics to the eval DB (eval_metric_snapshots table).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:422: * @param result - The BM25BaselineResult to persist.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:426:  result: BM25BaselineResult,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:466:   4. BM25 BASELINE RUNNER
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:470: * Run the BM25-only baseline measurement over the ground truth query set.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:473: * meaningful metrics. The injected `searchFn` must return results from
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:474: * the BM25/FTS5 path ONLY — vector, graph, and trigger channels must be
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:477: * For testing without a live DB, inject a mock `searchFn` that returns
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:482: * multi-strategy FTS5 matching (scripts/map-ground-truth-ids.ts).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:486: * @param searchFn - Injected BM25-only search function (dependency injection).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:488: * @returns        - BM25BaselineResult with metrics, timestamp, and contingency.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:490:export async function runBM25Baseline(
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:491:  searchFn: BM25SearchFn,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:492:  config: BM25BaselineConfig = {},
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:493:): Promise<BM25BaselineResult> {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:529:    // Run BM25-only search (channels: bm25/fts only, no vector/graph/trigger)
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:530:    const rawResults = await Promise.resolve(searchFn(q.query, fetchLimit));
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:556:  const metrics: BM25BaselineMetrics = {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.ts:588: * to real production memory IDs via FTS5 matching.
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:11:  '.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:15:  '001-memory-search-routing-tuning/001-search-fusion-tuning',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:16:  '001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:17:  '001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:18:  '001-memory-search-routing-tuning/001-search-fusion-tuning/003-continuity-search-profile',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:19:  '001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:20:  '001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:21:  '001-memory-search-routing-tuning/001-search-fusion-tuning/006-continuity-profile-validation',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:22:  '001-memory-search-routing-tuning/002-content-routing-accuracy',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:23:  '001-memory-search-routing-tuning/002-content-routing-accuracy/001-fix-delivery-progress-confusion',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:24:  '001-memory-search-routing-tuning/002-content-routing-accuracy/002-fix-handover-drop-confusion',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:25:  '001-memory-search-routing-tuning/002-content-routing-accuracy/003-wire-tier3-llm-classifier',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:26:  '001-memory-search-routing-tuning/002-content-routing-accuracy/004-doc-surface-alignment',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:27:  '001-memory-search-routing-tuning/002-content-routing-accuracy/005-task-update-merge-safety',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:28:  '001-memory-search-routing-tuning/002-content-routing-accuracy/006-tier3-prompt-enrichment',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:29:  '001-memory-search-routing-tuning/003-graph-metadata-validation',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:30:  '001-memory-search-routing-tuning/003-graph-metadata-validation/001-fix-status-derivation',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:31:  '001-memory-search-routing-tuning/003-graph-metadata-validation/002-sanitize-key-files',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:32:  '001-memory-search-routing-tuning/003-graph-metadata-validation/003-deduplicate-entities',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:33:  '001-memory-search-routing-tuning/003-graph-metadata-validation/004-normalize-legacy-files',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:34:  '001-memory-search-routing-tuning/003-graph-metadata-validation/005-doc-surface-alignment',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:35:  '001-memory-search-routing-tuning/003-graph-metadata-validation/006-key-file-resolution',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:36:  '001-memory-search-routing-tuning/003-graph-metadata-validation/007-entity-quality-improvements',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:66:        /010-search-and-routing-tuning|011-skill-advisor-graph|021-smart-router-context-efficacy/,
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:72:    const prompt = readText('001-memory-search-routing-tuning/001-search-fusion-tuning/prompts/deep-research-prompt.md');
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:74:      '.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:79:      '001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/plan.md',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:80:      '../../../../research/001-search-fusion-routing-research/research.md',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:83:      '001-memory-search-routing-tuning/002-content-routing-accuracy/002-fix-handover-drop-confusion/plan.md',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:84:      '../../../../research/002-content-routing-accuracy-research/research.md',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:88:      '../../research/019-system-hardening-pt-03/corpus/labeled-prompts.jsonl',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:93:      const text = readText(`001-memory-search-routing-tuning/002-content-routing-accuracy/004-doc-surface-alignment/${file}`);
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:99:  it('records completed smart-router research state under the current 004 lineage', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:101:      path.join(campaignRoot, '004-smart-router-context-efficacy/001-initial-research/research/deep-research-config.json'),
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:104:      'system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/004-smart-router-context-efficacy/001-initial-research',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:109:    const initialState = readText('004-smart-router-context-efficacy/001-initial-research/research/deep-research-state.jsonl');
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:111:      '"specFolder":"system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/004-smart-router-context-efficacy/001-initial-research"',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:117:      path.join(campaignRoot, '004-smart-router-context-efficacy/002-skill-md-intent-router-efficacy/research/deep-research-config.json'),
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:120:      'system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/004-smart-router-context-efficacy/002-skill-md-intent-router-efficacy',
.opencode/skills/system-spec-kit/mcp_server/tests/migration-lineage-identity.vitest.ts:125:    const childState = readText('004-smart-router-context-efficacy/002-skill-md-intent-router-efficacy/research/deep-research-state.jsonl');
.opencode/skills/system-spec-kit/mcp_server/lib/eval/k-value-analysis.ts:9:import { isRrfKExperimentalEnabled as _isRrfKExperimentalEnabled } from '../search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/eval/k-value-analysis.ts:127:/** K-values to test in the grid search. */
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.resume-gate-d.vitest.ts:30:vi.mock('../handlers/memory-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:5:  hybridRows: [] as Array<Record<string, unknown>>,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:24:  hybridSearchEnhanced: vi.fn(),
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:50:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:58:vi.mock('../lib/search/hybrid-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:61:  hybridSearchEnhanced: mocks.hybridSearchEnhanced,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:69:vi.mock('../lib/search/graph-search-fn', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:176:    mockState.hybridRows = [
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:226:    mocks.hybridSearchEnhanced.mockImplementation(async () => mockState.hybridRows);
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:238:    mocks.runAblation.mockImplementation(async (searchFn, config) => {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:239:      const results = await searchFn(
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:327:    const hybridSearchOptions = mocks.hybridSearchEnhanced.mock.calls[0]?.[2];
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:337:    expect(hybridSearchOptions).toMatchObject({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:346:    expect('includeArchived' in hybridSearchOptions).toBe(false);
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-ablation-drift.vitest.ts:347:    expect(hybridSearchOptions.triggerPhrases).toBeUndefined();
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:10:  searchWithFallback,
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:12:  hybridSearchEnhanced,
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:17:} from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:18:import type { HybridSearchResult, DegradationEvent } from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:19:import { isSearchFallbackEnabled } from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:118:    // When flag is OFF, searchWithFallback uses the original two-pass logic
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:122:    const result = await searchWithFallback('test query', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:127:  it('T045-05: searchWithFallback delegates to tiered when flag enabled', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:131:    const result = await searchWithFallback('test query', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:158:    // Initialize hybrid-search with our test db
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:233:    const results = await searchWithFallback('obscure query no results', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:246:    const results = await searchWithFallback('xyzzy nonsense query', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:262:    const results = await searchWithFallback('test degradation metadata', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/status.ts:41:    if (args.loopType !== 'research' && args.loopType !== 'review') {
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/status.ts:42:      return errorResponse('loopType must be "research" or "review"');
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-logger.ts:5:// Non-blocking, fail-safe logging hooks for search, context,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-logger.ts:8:// CRITICAL: Logging must NEVER break production search.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-logger.ts:38: * Generate a new eval_run_id for a single search invocation.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-logger.ts:134: * Log a search query to eval_queries.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-logger.ts:136: * Should be called at the entry point of each handler (search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/feedback-denylist.ts:63:  'result', 'results', 'query', 'search', 'find', 'get', 'set',
.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:48:  liveBaselineResolution: 'code_graph_query' | 'memory_context' | 'memory_context_then_grep';
.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:141:      return 'code_graph_query';
.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:143:    return 'memory_context_then_grep';
.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:146:  return 'memory_context';
.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:158:    if (resolution === 'code_graph_query') {
.opencode/skills/system-spec-kit/mcp_server/lib/eval/warm-start-variant-runner.ts:162:    if (resolution === 'memory_context_then_grep') {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:92: * For research: questions that have no incoming ANSWERS or COVERS edges.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:99:  const coverageRelations = loopType === 'research'
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:103:  const targetKinds = loopType === 'research'
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:143:    // Research mode: questions should have incoming ANSWERS edges.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:228:  const provenanceRelations = ns.loopType === 'research'
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:325: * For research: CLAIM nodes with status != 'verified'.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:332:  if (loopType === 'research') {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts:335:    // Research: CLAIM nodes where metadata.verification_status != 'verified'
.opencode/skills/system-spec-kit/mcp_server/tests/fsrs-scheduler.vitest.ts:227:  it('T048: Retrievability factor affects search ranking', () => {
.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts:5:import { isQualityAutoFixEnabled, isQualityLoopEnabled } from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts:91: * reliable retrieval via the `memory_match_triggers` tool. The scoring
.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts:757:  // Re-exported from search-flags for backward compatibility
.opencode/skills/system-spec-kit/mcp_server/lib/eval/shadow-scoring.ts:13:// CRITICAL: Shadow scoring must NEVER affect production search results.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/shadow-scoring.ts:240: * CRITICAL: Shadow scoring must NEVER affect production search results.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/shadow-scoring.ts:242: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/shadow-scoring.ts:265: * @param query - The original search query.
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator.vitest.ts:97:vi.mock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator.vitest.ts:141:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator.vitest.ts:147:import { closeDb, initializeDb } from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-boost.ts:6:import { isSessionBoostEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-boost.ts:34: * Delegates to the canonical flag check in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-boost.ts:225: * Session boost types exposed for search pipeline consumers.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:6:// Controlled ablation studies for search channel contribution analysis.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:7:// Selectively disables one search channel at a time, measures Recall@20
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:51:/** Known search channels that can be ablated. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:102: * A search function that the ablation runner calls for each query.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:105: * @param query - The search query text.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:162:  /** Error message returned by the failing search call. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:546: * The searchFn is called once per query per condition. It receives
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:550: * @param searchFn - Search function that respects channel disable flags.
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:555:  searchFn: AblationSearchFn,
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:600:      const results = await Promise.resolve(searchFn(q.query, noDisabled));
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:627:          const results = await Promise.resolve(searchFn(q.query, disabledSet));
.opencode/skills/system-spec-kit/mcp_server/lib/eval/ablation-framework.ts:995: * expected by the hybridSearch / hybridSearchEnhanced functions.
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-ux-regressions.vitest.ts:30:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:14:} from '../lib/search/query-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:21:} from '../lib/search/channel-representation';
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:30:} from '../lib/search/confidence-truncation';
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:37:} from '../lib/search/dynamic-token-budget';
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:5:// research and review convergence metrics.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:36:export interface ResearchConvergenceSignals {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:52:export type ConvergenceSignals = ResearchConvergenceSignals | ReviewConvergenceSignals;
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:62:type ResearchSignalNodeLike = {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:68:type ResearchSignalEdgeLike = {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:206: * Compute research convergence signals.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:208:export function computeResearchSignals(ns: Namespace): ResearchConvergenceSignals {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:212:  const questionCoverage = computeResearchQuestionCoverageFromData(nodes, edges);
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:213:  const claimVerificationRate = computeResearchClaimVerificationRateFromData(nodes);
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:214:  const contradictionDensity = computeResearchContradictionDensityFromData(edges);
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:215:  const sourceDiversity = computeResearchSourceDiversityFromData(nodes, edges);
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:216:  const evidenceDepth = computeResearchEvidenceDepthFromData(nodes, edges);
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:240:function buildAnsweringFindingsByQuestion(edges: ReadonlyArray<ResearchSignalEdgeLike>): Map<string, string[]> {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:252:function buildCitedSourcesByFinding(edges: ReadonlyArray<ResearchSignalEdgeLike>): Map<string, string[]> {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:265: * Canonical research question coverage: questions with at least two ANSWERS
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:266: * edges divided by all research questions in the graph.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:268:export function computeResearchQuestionCoverageFromData(
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:269:  nodes: ReadonlyArray<ResearchSignalNodeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:270:  edges: ReadonlyArray<ResearchSignalEdgeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:291: * Canonical research claim verification rate: verified claims divided by all
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:295:export function computeResearchClaimVerificationRateFromData(
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:296:  nodes: ReadonlyArray<ResearchSignalNodeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:313: * Canonical research contradiction density: CONTRADICTS edges divided by all
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:314: * research edges in the graph.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:316:export function computeResearchContradictionDensityFromData(
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:317:  edges: ReadonlyArray<ResearchSignalEdgeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:330: * Canonical research source diversity: for each question, count distinct
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:334:export function computeResearchSourceDiversityFromData(
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:335:  nodes: ReadonlyArray<ResearchSignalNodeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:336:  edges: ReadonlyArray<ResearchSignalEdgeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:375: * Canonical research evidence depth: average path length across all
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:379:export function computeResearchEvidenceDepthFromData(
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:380:  nodes: ReadonlyArray<ResearchSignalNodeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:381:  edges: ReadonlyArray<ResearchSignalEdgeLike>,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:547: * Dispatches to research or review signal computation based on loop type.
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:550:  if (ns.loopType === 'research') {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts:551:    return computeResearchSignals(ns);
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-integration.vitest.ts:10:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-integration.vitest.ts:185:    '      - "research/research.md"',
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:8:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:11:  hybridSearchEnhanced,
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:14:} from '../lib/search/hybrid-search.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:42:} from '../lib/search/graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:43:import { isDegreeBoostEnabled } from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:266:    const searchFn: AblationSearchFn = async (query, disabledChannels) => {
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:270:      const searchOptions = {
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:281:      const results = await hybridSearchEnhanced(query, embedding, searchOptions);
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:291:    return runAblation(searchFn, {
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:332:  'hybrid search fusion',
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:335:  'semantic search',
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts:341: * 1. Runs hybridSearchEnhanced for each representative query
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:96:      validateToolInputSchema('memory_context', {}, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:132:      validateToolInputSchema('memory_context', { input: 'resume', mode: 'invalid-mode' }, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:146:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:150:    expect(errorSpy.mock.calls.some((call) => String(call[0]).includes('[schema-validation] memory_search:'))).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:286:   4. memory_search LIMIT CONTRACT (schema + runtime alignment)
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:289:describe('memory_search limit contract', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:292:      validateToolInputSchema('memory_search', { cursor: 'opaque-cursor-token' }, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:298:      validateToolArgs('memory_search', { cursor: 'opaque-cursor-token' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:302:  it('public schema accepts concepts-only search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:304:      validateToolInputSchema('memory_search', { concepts: ['alpha', 'beta'] }, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:310:      validateToolInputSchema('memory_search', {}, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:316:      validateToolArgs('memory_search', { query: 'ab', limit: 100 });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:322:      validateToolArgs('memory_search', { query: 'ab', limit: 101 });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:328:      validateToolInputSchema('memory_search', { query: 'ab', limit: 101 }, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:334:      validateToolArgs('memory_search', { concepts: ['solo'] });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:338:  it('public schema rejects unknown memory_search parameters', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:340:      validateToolInputSchema('memory_search', { query: 'valid query', unexpected: true }, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:346:      validateToolInputSchema('memory_search', { query: 'a' }, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:350:  it('runtime rejects unknown memory_search parameters', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:352:      validateToolArgs('memory_search', { query: 'valid query', unexpected: true } as Record<string, unknown>);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:356:  it('runtime accepts governed scope fields for memory_search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:358:      validateToolArgs('memory_search', {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:367:  it('public and runtime schemas accept response profiles for memory_search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:374:      validateToolInputSchema('memory_search', args, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:376:    expect(validateToolArgs('memory_search', args)).toEqual(args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:381:  it('public and runtime schemas accept governed scope fields for memory_context', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:390:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:392:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:395:  it('public and runtime schemas accept response profiles for memory_context', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:402:      validateToolInputSchema('memory_context', args, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:404:    expect(validateToolArgs('memory_context', args)).toEqual(args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:407:  it('public and runtime schemas accept governed scope fields for memory_quick_search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:416:      validateToolInputSchema('memory_quick_search', args, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:418:    expect(validateToolArgs('memory_quick_search', args)).toEqual(args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:421:  it('public and runtime schemas accept governed scope fields for memory_match_triggers', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:431:      validateToolInputSchema('memory_match_triggers', args, TOOL_DEFINITIONS);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:433:    expect(validateToolArgs('memory_match_triggers', args)).toEqual(args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:503:      name: 'code_graph_query accepts structural traversal options',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:504:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:516:      name: 'code_graph_query accepts minConfidence within [0, 1] (R-007-6)',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:517:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:525:      name: 'code_graph_query accepts minConfidence boundary value 0',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:526:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:534:      name: 'code_graph_query accepts minConfidence boundary value 1',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:535:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:548:      name: 'code_graph_context accepts seed payloads',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:549:      toolName: 'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:572:      name: 'code_graph_query rejects unknown operations',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:573:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:580:      name: 'code_graph_query rejects minConfidence above 1 (R-007-6)',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:581:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:589:      name: 'code_graph_query rejects negative minConfidence (R-007-6)',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:590:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:598:      name: 'code_graph_query rejects non-numeric minConfidence (R-007-6)',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:599:      toolName: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:614:      name: 'code_graph_context rejects unsupported profiles',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-input-schema.vitest.ts:615:      toolName: 'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-metrics.ts:11:/** A single retrieved result from a search query. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-metrics.ts:15:  /** Retrieval score assigned by the search system. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-quality-proxy.ts:48:  /** Number of results actually returned by the search. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-quality-proxy.ts:53:   * passed to the search call).
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-quality-proxy.ts:58:  /** Actual search latency in milliseconds. */
.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-quality-proxy.ts:151: * Compute the quality proxy score for a single search result set.
.opencode/skills/system-spec-kit/mcp_server/tests/spec-doc-structure.vitest.ts:70:function replaceText(filePath: string, searchValue: string, replaceValue: string): void {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-doc-structure.vitest.ts:72:  fs.writeFileSync(filePath, content.replace(searchValue, replaceValue), 'utf8');
.opencode/skills/system-spec-kit/mcp_server/tests/spec-doc-structure.vitest.ts:132:  it('freezes the failure-code ordering from Gate C research', () => {
.opencode/skills/system-spec-kit/mcp_server/lib/search/surrogate-storage.ts:10:// Surrogate storage is populated at index time and queried at search time via
.opencode/skills/system-spec-kit/mcp_server/handlers/pe-gating.ts:4:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/pe-gating.ts:9:import { classifyEncodingIntent } from '../lib/search/encoding-intent.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/pe-gating.ts:10:import { isEncodingIntentEnabled } from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/pe-gating.ts:171:    console.warn('[PE-Gate] Vector search failed:', message);
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:17:export type LoopType = 'research' | 'review';
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:19:/** Research node kinds */
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:20:export type ResearchNodeKind = 'QUESTION' | 'FINDING' | 'CLAIM' | 'SOURCE';
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:26:export type NodeKind = ResearchNodeKind | ReviewNodeKind;
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:28:/** Research edge relation types */
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:29:export type ResearchRelation =
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:50:export type Relation = ResearchRelation | ReviewRelation;
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:113:/** Initial weight estimates for research relations */
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:114:export const RESEARCH_WEIGHTS: Record<ResearchRelation, number> = {
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:138:  research: ['QUESTION', 'FINDING', 'CLAIM', 'SOURCE'] as const,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:144:  research: ['ANSWERS', 'SUPPORTS', 'CONTRADICTS', 'SUPERSEDES', 'DERIVED_FROM', 'COVERS', 'CITES'] as const,
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts:159:    loop_type TEXT NOT NULL CHECK(loop_type IN ('research', 'review')),
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index.ts:25:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index.ts:558:            AND document_type IN ('spec', 'plan', 'tasks', 'checklist', 'decision_record', 'implementation_summary', 'research', 'handover', 'graph_metadata')
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:15:} from '../lib/search/recovery-payload';
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:183:      query: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:201:      query: 'implementation details for hybrid rag fusion pipeline',
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:223:      query: 'implementation details for hybrid rag fusion pipeline',
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:232:      query: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:279:    const payload = buildRecoveryPayload(makeCtx({ query: 'hybrid rag fusion pipeline' }));
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:284:    const payload = buildRecoveryPayload(makeCtx({ query: 'hybrid rag fusion pipeline implementation' }));
.opencode/skills/system-spec-kit/mcp_server/tests/d5-recovery-payload.vitest.ts:301:      query: 'implementation details for hybrid rag fusion pipeline stage two',
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:3:import * as searchHandler from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:23:    it('T531-1: sessionId parameter accepted by search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:26:          searchHandler.handleMemorySearch({
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:39:    it('T531-2: enableDedup=true accepted by search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:42:          searchHandler.handleMemorySearch({
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:78:          searchHandler.handleMemorySearch({
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:97:          searchHandler.handleMemorySearch({
.opencode/skills/system-spec-kit/mcp_server/tests/integration-session-dedup.vitest.ts:113:          searchHandler.handleMemorySearch({
.opencode/skills/system-spec-kit/mcp_server/tests/usage-weighted-ranking.vitest.ts:6:vi.mock('../lib/search/search-flags.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/usage-weighted-ranking.vitest.ts:12:import { isUsageRankingEnabled } from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/session-bootstrap.vitest.ts:126:    recommendedAction: 'Structural context available. Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/tests/session-bootstrap.vitest.ts:197:      'Structural context available. Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:46:} from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:69:import { delete_memory_from_database } from '../lib/search/vector-index-mutations.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:207:type CanonicalPacketKind = 'feature' | 'phase' | 'remediation' | 'research' | 'unknown';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:233:  'research_finding',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:996:  if (packetType === 'research') {
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:997:    return 'research';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:1261:    research_finding: 'Review cited finding',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:1742:      description: 'Run incremental spec-doc indexing so the save is immediately searchable.',
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:2719:    throw new Error('File must be a canonical spec document under specs/**/ (spec.md, plan.md, tasks.md, checklist.md, decision-record.md, implementation-summary.md, handover.md, research.md, resource-map.md, description.json, graph-metadata.json) or a constitutional memory under .opencode/skills/*/constitutional/');
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:3086:      // (vec_memories, BM25 index, causal edges, projections, etc.)
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:3087:      // not just memory_index, to prevent orphaned search phantoms.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:175:// Graph calibration gate — canonical implementation in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:177:import { isGraphCalibrationProfileEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:260: * @param searchFn   - Search function accepting disabled feature set.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:266:  searchFn: AblationSearchFn,
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:272:  const baseline = measureAllIntents(searchFn, queries, new Set(), k, 'baseline');
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:279:    const result = measureAllIntents(searchFn, queries, disabled, k, toggle.name);
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:290:  searchFn: AblationSearchFn,
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts:299:    const results = searchFn(query.query, disabledFeatures);
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-stats.ts:13:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-stats.ts:16:import { getGraphMetrics } from '../lib/search/hybrid-search.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-stats.ts:295:    hints.push('Vector search unavailable - using BM25 fallback');
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:7:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:9:import * as bm25Index from '../lib/search/bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:14:import { classifyEncodingIntent } from '../lib/search/encoding-intent.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:15:import { isEncodingIntentEnabled, type SavePlannerMode } from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:365:      // BM25 index the chunk
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:377:          console.error(`[memory-save] BM25 indexing failed for chunk ${i + 1}: ${message}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:459:        console.warn(`[memory-save] BM25 rollback failed for chunk(s) of parent ${parentId}: ${message}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:468:        console.warn(`[memory-save] BM25 rollback failed for parent ${parentId}: ${message}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:600:  // T332: Update parent BM25 only after at least one chunk succeeds and
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:613:      console.warn(`[memory-save] BM25 indexing failed for parent: ${message}`);
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:653:      (bm25FailedChunks.length > 0 ? ` (${bm25FailedChunks.length} BM25 failures)` : ''),
.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:34:      hybridSearch: { init: vi.fn() },
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-decay-policy.vitest.ts:64:    expect(HYBRID_NO_DECAY_CONTEXT_TYPES.has('research')).toBe(false);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-decay-policy.vitest.ts:91:  it('classifies research as fsrs_schedule', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-decay-policy.vitest.ts:92:    expect(classifyHybridDecay('research')).toBe('fsrs_schedule');
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-decay-policy.vitest.ts:152:    expect(applyHybridDecayPolicy(stability, 'research')).toBe(stability);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-decay-policy.vitest.ts:195:    // When hybrid decay is OFF but classification decay is ON, applyHybridDecayPolicy
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:4:import * as hybridSearch from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:5:import * as bm25Index from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:13:// Mock documents for testing - each has >10 words for BM25 MIN_DOC_LENGTH requirement
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:14:type InitDb = Parameters<typeof hybridSearch.init>[0];
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:15:type VectorSearchFn = NonNullable<Parameters<typeof hybridSearch.init>[1]>;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:16:type GraphSearchFn = NonNullable<Parameters<typeof hybridSearch.init>[2]>;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:17:type HybridSearchResult = Awaited<ReturnType<typeof hybridSearch.hybridSearchEnhanced>>[number];
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:18:type MaybeAsyncHybridResults = ReturnType<typeof hybridSearch.hybridSearchEnhanced> | HybridSearchResult[];
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:19:type HybridModuleExport = keyof typeof hybridSearch;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:37:// Mock vector search function
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:53:// Mock graph search function
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:62:const ORIGINAL_ENABLE_BM25 = process.env.ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:64:// Mock database with FTS5 table
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:71:            return { count: 1 }; // FTS5 table exists
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:196:): value is ReturnType<typeof hybridSearch.hybridSearchEnhanced> {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:206:    process.env.ENABLE_BM25 = 'true';
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:210:    if (ORIGINAL_ENABLE_BM25 === undefined) {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:211:      delete process.env.ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:213:      process.env.ENABLE_BM25 = ORIGINAL_ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:224:          hybridSearch.init(null as unknown as InitDb, mockVectorSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:232:        hybridSearch.init(mockDb, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:236:    it('T031-INIT-03: init() accepts optional graph search function', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:239:        hybridSearch.init(mockDb, mockVectorSearch, mockGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:243:    it('T031-INIT-04: init() works without graph search function', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:246:        hybridSearch.init(mockDb, mockVectorSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:251:  // 5.2 BM25 SEARCH TESTS
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:253:  describe('BM25 Search Tests (T031)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:259:    it('T031-BM25-01: is_bm25_available() returns false when empty', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:260:      const available = hybridSearch.isBm25Available();
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:264:    it('T031-BM25-02: is_bm25_available() returns true when populated', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:269:      const available = hybridSearch.isBm25Available();
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:273:    it('T031-BM25-03: bm25_search() returns results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:278:      const results = hybridSearch.bm25Search('authentication', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:283:    it('T031-BM25-04: bm25_search() results have score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:288:      const results = hybridSearch.bm25Search('authentication', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:293:    it('T031-BM25-05: bm25_search() respects limit option', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:298:      const results = hybridSearch.bm25Search('authentication', { limit: 2 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:302:    it('T031-BM25-06: bm25_search() respects spec_folder filter', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:307:      const results = hybridSearch.bm25Search('module', { limit: 10, specFolder: 'specs/auth' });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:316:    it('T031-BM25-07: bm25_search() fails closed when scoped lookup throws', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:347:      hybridSearch.init(failingDb, mockVectorSearch, mockGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:353:      const results = hybridSearch.bm25Search('module', { limit: 10, specFolder: 'specs/auth' });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:357:        '[BM25] Spec-folder scope lookup failed, returning empty scoped results:',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:369:      hybridSearch.init(mockDb, mockVectorSearch, mockGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:377:    it('T031-LEX-01: combined_lexical_search() returns results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:378:      const results = hybridSearch.combinedLexicalSearch('authentication', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:383:    it('T031-LEX-02: combined_lexical_search() results have score field', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:384:      const results = hybridSearch.combinedLexicalSearch('authentication', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:389:    it('T031-LEX-03: combined_lexical_search() handles source tracking', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:390:      const results = hybridSearch.combinedLexicalSearch('authentication', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:399:    it('T031-LEX-04: combined_lexical_search() deduplicates by ID', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:400:      const results = hybridSearch.combinedLexicalSearch('authentication module', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:406:    it('T031-LEX-05: combined_lexical_search() deduplicates canonical IDs', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:407:      const results = hybridSearch.combinedLexicalSearch('authentication module', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:409:        hybridSearch.__testables.canonicalResultId(r.id as number | string)
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:415:    it('T031-LEX-05: combined_lexical_search() results sorted by score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:416:      const results = hybridSearch.combinedLexicalSearch('authentication', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:436:      hybridSearch.init(mockDb, mockVectorSearch, mockGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:445:    it('T031-HYB-01: hybridSearchEnhanced() returns results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:446:      const result = hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 5 }) as MaybeAsyncHybridResults;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:452:    it('T031-HYB-02: hybridSearchEnhanced() returns correct type', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:453:      const result = hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 5 }) as MaybeAsyncHybridResults;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:458:    it('T031-HYB-03: hybridSearchEnhanced() accepts useBm25=true', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:460:        hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 5, useBm25: true });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:464:    it('T031-HYB-04: hybridSearchEnhanced() accepts useBm25=false', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:466:        hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 5, useBm25: false });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:470:    it('T031-HYB-05: hybridSearchEnhanced() results have scores', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:471:      const result = hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 5 }) as MaybeAsyncHybridResults;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:483:    it('T031-HYB-06: hybridSearchEnhanced() has source tracking', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:484:      const results = await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:493:    it('T031-HYB-07: hybridSearchEnhanced() respects limit option', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:494:      const results = await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:500:    it('T031-HYB-08: hybridSearchEnhanced() filters results by specFolder', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:502:      const results = await hybridSearch.hybridSearchEnhanced('module', mockEmbedding, { limit: 10, specFolder: 'specs/auth' });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:512:    it('T031-HYB-09: hybridSearchEnhanced() accepts query string', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:513:      const results = await hybridSearch.hybridSearchEnhanced('test query', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:518:    it('T031-HYB-10: hybridSearchEnhanced() works with null embedding', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:520:        hybridSearch.hybridSearchEnhanced('test', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:529:        const results = await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:554:      hybridSearch.init(mockDb, mockVectorSearch, mockGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:558:    it('T031-RRF-01: unified_search available from rrf-fusion', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:571:    it('T031-RRF-04: hybridSearchEnhanced uses RRF fusion internally', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:573:        hybridSearch.hybridSearchEnhanced('test', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:586:      hybridSearch.init(mockDb, mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:590:    it('T031-BASIC-01: hybridSearch() returns result', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:591:      const result = hybridSearch.hybridSearch('authentication', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:595:    it('T031-BASIC-02: hybridSearch() returns correct type', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:596:      const result = hybridSearch.hybridSearch('authentication', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:600:    it('T031-BASIC-03: hybridSearch() has source tracking', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:602:        hybridSearch.hybridSearch('authentication', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:606:    it('T031-BASIC-04: hybridSearch() deduplicates canonical IDs across channels', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:613:      const results = await hybridSearch.hybridSearch('authentication module', null, {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:620:      const canonicalIds = results.map((r) => hybridSearch.__testables.canonicalResultId(r.id));
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:634:      hybridSearch.init(mockDb, mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:638:    it('T031-FALL-01: searchWithFallback() returns result', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:639:      const result = hybridSearch.searchWithFallback('authentication', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:643:    it('T031-FALL-02: searchWithFallback() handles null embedding', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:645:        hybridSearch.searchWithFallback('authentication', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:650:  // 5.8 FTS SEARCH TESTS
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:652:  describe('FTS5 Search Tests', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:656:      hybridSearch.init(mockDb, mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:659:    it('T031-FTS-01: is_fts_available() returns boolean', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:660:      const available = hybridSearch.isFtsAvailable();
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:664:    it('T031-FTS-02: fts_search() returns array', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:665:      const results = hybridSearch.ftsSearch('authentication', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:669:    it('T031-FTS-03: fts_search() results have fts_score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:670:      const results = hybridSearch.ftsSearch('authentication', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:678:    it('T031-FTS-04: fts_search() escapes special characters', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:679:      const results = hybridSearch.ftsSearch('test*:query()', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:683:    it('T031-FTS-05: fts_search() escapes boolean operators', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:684:      const results = hybridSearch.ftsSearch('test AND query OR something NOT here', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:697:      'hybridSearch',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:698:      'hybridSearchEnhanced',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:699:      'searchWithFallback',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:707:        expect(hybridSearch[name]).toBeDefined();
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:716:    it('T031-ERR-01: hybridSearchEnhanced() with valid init works', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:718:      hybridSearch.init(mockDb, mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:721:        hybridSearch.hybridSearchEnhanced('test', mockEmbedding, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:725:    it('T031-ERR-02: bm25_search() handles empty/disabled state gracefully', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:727:      const results = hybridSearch.bm25Search('test', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:731:    it('T031-ERR-03: fts_search() handles empty query', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:733:      hybridSearch.init(mockDb, mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:734:      const results = hybridSearch.ftsSearch('', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:739:    it('T031-ERR-04: combined_lexical_search() handles no results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:740:      const results = hybridSearch.combinedLexicalSearch('xyzzy123nonexistent', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:747:  it('C138-T1: hybridSearch module exports hybridSearchEnhanced (pipeline entry)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:748:    expect(typeof hybridSearch.hybridSearchEnhanced).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:751:  it('C138-T2: hybridSearch module exports init function', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:752:    expect(typeof hybridSearch.init).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:789:    hybridSearch.init(mockDb, mockVectorSearch, trackingGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:807:    // No explicit useGraph option → should default to true and invoke graph search
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:808:    await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:813:    await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 10, useGraph: false });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:818:    const results = await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 20 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:819:    // Since graph search returns results, at least some should come from graph or be fused
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:824:    hybridSearch.resetGraphMetrics();
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:825:    await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:826:    const metrics = hybridSearch.getGraphMetrics();
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:834:    const results = await hybridSearch.hybridSearchEnhanced('authentication', mockEmbedding, { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:840:describe('C138-P0: Adaptive Fallback in searchWithFallback', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:842:    // Use a vector search that returns nothing to force fallback scenarios
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:845:    // Init with empty search functions — will rely on FTS/BM25 from mock DB
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:846:    hybridSearch.init(mockDb, emptyVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:848:    // BM25 is empty, FTS from mock returns results, so primary should return results
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:849:    const results = await hybridSearch.searchWithFallback('authentication', null, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:850:    // Should get results from FTS at minimum (via mock DB)
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:869:        hybridSearch.init(mockDb, lowRecallVectorSearch as VectorSearchFn, trackingGraphSearch as GraphSearchFn);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:881:      await hybridSearch.searchWithFallback('auth', embedding, { limit: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:916:  it('T020: searchWithFallback uses percentage minSimilarity thresholds for adaptive retry', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:924:    hybridSearch.init(createMockDb(), recordingVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:926:    const results = await hybridSearch.searchWithFallback(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:936:  it('T020: collectRawCandidates tiered fallback widens vector search with 30/10 percent floors', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:945:    hybridSearch.init(createMockDb(), recordingVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:947:    await hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:965:    hybridSearch.init(createMockDb(), thresholdAwareVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:967:    const results = await hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:984:    hybridSearch.init(createMockDb(), emptyVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:991:    const results = await hybridSearch.searchWithFallback(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1012:    hybridSearch.init(createMockDb(), thresholdAwareVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1015:      const results = await hybridSearch.searchWithFallback(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1030:  const { mergeRawCandidate } = hybridSearch.__testables;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1117:    hybridSearch.init(degreeAwareDb, vectorOnlySearch, () => []);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1120:    const results = await hybridSearch.hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1143:    hybridSearch.init(degreeAwareDb, vectorOnlySearch, () => [{ id: 2, score: 0.7 }]);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1146:    const results = await hybridSearch.hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1169:    hybridSearch.init(mockDb, mockVectorSearch, graphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1176:    const results = await hybridSearch.hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1232:      hybridSearch.init(mmrDb, vectorWithEmbeddings, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1235:      const results = await hybridSearch.hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1305:    hybridSearch.init(promotionDb, vectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1313:    const results = await hybridSearch.hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1338:    expect(hybridSearch.estimateResultTokens(enrichedResult)).toBeGreaterThan(
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1339:      hybridSearch.estimateResultTokens(baseResult)
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1360:    const budget = hybridSearch.estimateResultTokens(compact) + 5;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1362:    const truncated = hybridSearch.truncateToBudget([oversized, compact], budget, {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1393:    const truncated = hybridSearch.truncateToBudget([oversizedSecond, oversizedTop], 50, {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1419:    const truncated = hybridSearch.truncateToBudget([resultWithGetter], 1, {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1447:  it('S1-FIX-01: routeQuery trigger-phrase path is reachable from hybridSearchEnhanced', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1450:    hybridSearch.init(mockDb, mockVectorSearch, mockGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1454:    const results = await hybridSearch.hybridSearchEnhanced(longTrigger, embedding, {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1466:  it('S1-FIX-02: folder scoring integrates into hybrid runtime behind feature flag', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1470:    hybridSearch.init(mockDb, mockVectorSearch, mockGraphSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1473:    const results = await hybridSearch.hybridSearchEnhanced('authentication module', embedding, { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1483:  it('S1-FIX-03: dynamic token budget is applied to live hybrid results', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1498:    hybridSearch.init(mockDb, hugeVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1501:    const results = await hybridSearch.hybridSearchEnhanced('fix bug', embedding, { limit: 20 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1527:    hybridSearch.init(mockDb, hugeVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1530:    const results = await hybridSearch.hybridSearchEnhanced('fix bug', embedding, {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1561:    hybridSearch.init(mockDb, trackingVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1569:  it('BUG1-T1: useVector=false prevents vector search function from being called', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1571:    await hybridSearch.hybridSearchEnhanced('authentication', embedding, { limit: 10, useVector: false });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1575:  it('BUG1-T2: useVector=true (default) calls vector search function', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1577:    await hybridSearch.hybridSearchEnhanced('authentication', embedding, { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1581:  it('BUG1-T3: useFts=false removes FTS results from output', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1583:    const results = await hybridSearch.hybridSearchEnhanced('authentication', embedding, { limit: 10, useFts: false });
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1588:  it('BUG1-T4: useBm25=false removes BM25 results from output', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts:1590:    const results = await hybridSearch.hybridSearchEnhanced('authentication', embedding, { limit: 10, useBm25: false });
.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:9:import * as vectorIndex from '../search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-tools.vitest.ts:12:    content: [{ type: 'text', text: JSON.stringify({ data: { results: [], count: 0 }, meta: { tool: 'memory_search' } }) }],
.opencode/skills/system-spec-kit/mcp_server/tests/memory-tools.vitest.ts:41:  it('forwards governed scope fields through memory_quick_search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-tools.vitest.ts:42:    const response = await handleTool('memory_quick_search', {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-tools.vitest.ts:64:    expect(parsed.meta?.tool).toBe('memory_quick_search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:18:import { isEmbeddingExpansionEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:38: *                     use as a search query in downstream channels.
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:165: *   4. Vector search returns no candidates with content.
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:168: *   a. Run a vector similarity search using the provided embedding.
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:211:    // -- Step a: Vector similarity search --------------------------------------
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:267:    // FTS and embedding re-encoding without requiring a separator token.
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:297: * @param query - The candidate search query.
.opencode/skills/system-spec-kit/mcp_server/tests/session-learning-regressions.vitest.ts:6:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-lifecycle.ts:23:import { clearDegreeCacheForDb } from './graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-lifecycle.ts:81:// REQ-D3-004: LLM graph backfill gate — canonical implementation in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-lifecycle.ts:86:} from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/providers/README.md:51:| **Graceful Degradation** | Falls back to BM25-only mode when all providers fail |
.opencode/skills/system-spec-kit/mcp_server/lib/providers/README.md:209:| [search/README.md](../search/README.md) | Vector search using embeddings |
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:4:// MCP tool handler for code_graph_query — queries structural relationships.
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:196:  nextTool: 'code_graph_scan' | 'code_graph_query' | 'rg';
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:828:    }, readiness, `code_graph_query ${operation} blocked payload`),
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1078:/** Handle code_graph_query tool call */
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1096:    // as code_graph_context. Previously this path dropped the readiness
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1179:          }, readiness, 'code_graph_query outline payload'),
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1256:              }, readiness, 'code_graph_query blast_radius fallback payload'),
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1285:            }, readiness, 'code_graph_query blast_radius ambiguity payload'),
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1312:            }, readiness, 'code_graph_query blast_radius empty-source payload'),
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1376:          }, readiness, 'code_graph_query blast_radius payload'),
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1423:          }, readiness, `code_graph_query ${operation} payload`),
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts:1493:          }, readiness, `code_graph_query ${operation} payload`, summarizeWeakestGraphEdgeEnrichment(result.edges)),
.opencode/skills/system-spec-kit/mcp_server/tests/causal-boost.vitest.ts:4:import * as causalBoost from '../lib/search/causal-boost';
.opencode/skills/system-spec-kit/mcp_server/tests/causal-boost.vitest.ts:5:import type { RankedSearchResult } from '../lib/search/causal-boost';
.opencode/skills/system-spec-kit/mcp_server/tests/quality-loop.vitest.ts:46:This memory documents the Sprint 0 measurement foundation for the hybrid RAG fusion refinement project.
.opencode/skills/system-spec-kit/mcp_server/tests/quality-loop.vitest.ts:53:- Implemented fail-safe logging that never breaks production search
.opencode/skills/system-spec-kit/mcp_server/tests/quality-loop.vitest.ts:55:- Added BM25 baseline with configurable k1/b parameters
.opencode/skills/system-spec-kit/mcp_server/tests/quality-loop.vitest.ts:60:- Implement hybrid fusion scoring calibration
.opencode/skills/system-spec-kit/mcp_server/tests/retrieval-directives.vitest.ts:18:} from '../lib/search/retrieval-directives';
.opencode/skills/system-spec-kit/mcp_server/tests/retrieval-directives.vitest.ts:24:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:203:    it('research node types are well-defined', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:204:      const researchNodeTypes = ['question_node', 'finding_node', 'claim_node', 'source_node'];
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:205:      expect(researchNodeTypes.length).toBe(4);
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:206:      for (const type of researchNodeTypes) {
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:221:    it('research relations are well-defined', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:222:      const researchRelations = ['ANSWERS', 'CONTRADICTS', 'CITES', 'EXTENDS', 'SUPERSEDES'];
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:223:      expect(researchRelations.length).toBe(5);
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts:224:      for (const rel of researchRelations) {
.opencode/skills/system-spec-kit/mcp_server/lib/providers/embeddings.ts:4:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-tools.vitest.ts:138:    it('includes optional research-specific signal', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-tools.vitest.ts:259:    it('research relation weights fall within valid range', () => {
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:228: * `.opencode/commands/memory/search.md` §4A mandates that confidence below 0.30
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:235: * "search" appear in NO keyword table.
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:275:  security_audit: { recency: 0.1, importance: 0.5, similarity: 0.4, contextType: 'research' },
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:657: * Apply intent-based weight adjustments to search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:659: * @param results - Array of search result records
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:706: * Get search query weights based on detected intent.
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:761:const INTENT_TO_PROFILE: Readonly<Record<IntentType, 'quick' | 'research' | 'debug'>> = {
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:764:  understand: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:765:  find_spec: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:766:  find_decision: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:777:function getProfileForIntent(intent: IntentType): 'quick' | 'research' | 'debug' | null {
.opencode/skills/system-spec-kit/mcp_server/tests/memory/trust-badges.test.ts:10:} from '../../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/promotion-positive-validation-semantics.vitest.ts:13:} from '../lib/search/auto-promotion';
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/README.md:12:| `query.ts` | `code_graph_query` | Run structural relationship reads (`outline`, `calls_*`, `imports_*`, `blast_radius`) with shared readiness/trust metadata, explicit blocked-read payloads when a full scan is required, and warnings for ambiguous subjects or dangling edges |
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/README.md:14:| `context.ts` | `code_graph_context` | Build LLM-oriented graph neighborhoods from manual, graph, or CocoIndex seeds; successful responses include anchors, graph context, and `metadata.partialOutput`, while full-scan-required reads return an explicit blocked payload with `requiredAction: "code_graph_scan"` |
.opencode/skills/system-spec-kit/mcp_server/tests/search-limits-scoring.vitest.ts:7:import * as crossEncoder from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/interfaces.vitest.ts:24:  async search(embedding: Float32Array, topK: number): Promise<any[]> {
.opencode/skills/system-spec-kit/mcp_server/tests/interfaces.vitest.ts:243:        await base.search(null, 10);
.opencode/skills/system-spec-kit/mcp_server/tests/interfaces.vitest.ts:252:      expect(typeof mock.search).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/interfaces.vitest.ts:274:    it('MockVectorStore.search() finds inserted records', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/interfaces.vitest.ts:284:      const results = await mock.search(embedding1, 10);
.opencode/skills/system-spec-kit/mcp_server/tests/interfaces.vitest.ts:480:      // Requires: import { SQLiteVectorStore } from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/search/memory-summaries.ts:4:// Feature catalog: Memory summary search channel
.opencode/skills/system-spec-kit/mcp_server/lib/search/memory-summaries.ts:9:import { isMemorySummariesEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/memory-summaries.ts:148: * Vector search on summary embeddings — parallel channel for stage1.
.opencode/skills/system-spec-kit/mcp_server/lib/search/memory-summaries.ts:159: * @returns Array of summary search results sorted by similarity descending
.opencode/skills/system-spec-kit/mcp_server/lib/search/memory-summaries.ts:204: * Used to determine if the summary search channel should be activated
.opencode/skills/system-spec-kit/mcp_server/tests/context-metrics.vitest.ts:60:    it('increments codeGraphQueries on code_graph_query event', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-metrics.vitest.ts:62:      recordMetricEvent({ kind: 'code_graph_query' });
.opencode/skills/system-spec-kit/mcp_server/lib/contracts/README.md:106:| `query` | `string` | The search query string |
.opencode/skills/system-spec-kit/mcp_server/lib/contracts/README.md:188:- Ranking confidence from `lib/search/confidence-scoring.ts` is retrieval-ordering metadata only and must not be reused as `StructuralTrust`.
.opencode/skills/system-spec-kit/mcp_server/lib/contracts/README.md:264:| [lib/search/README.md](../search/README.md) | Hybrid search pipeline |
.opencode/skills/system-spec-kit/mcp_server/lib/contracts/README.md:271:| `handlers/memory-search.ts` | Primary consumer of `ContextEnvelope` |
.opencode/skills/system-spec-kit/mcp_server/lib/contracts/README.md:281:Packet `007-detector-provenance-and-regression-floor` treats frozen detector fixtures as a regression-integrity floor only. The acceptance criterion from research recommendation R6 is the governing boundary: Public must land frozen detector fixtures that fail on structural regressions, while follow-on task corpora for user-visible structural quality are defined separately.
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-reconsolidation.vitest.ts:17:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-reconsolidation.vitest.ts:26:vi.mock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-reconsolidation.vitest.ts:45:vi.mock('../lib/search/encoding-intent', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-reconsolidation.vitest.ts:49:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:6:} from '../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:68:    spec_folder: 'specs/system-spec-kit/022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:85:    'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:133:      specFolder: 'specs/system-spec-kit/022-hybrid-rag-fusion/filters/fusion-only',
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:237:        query: 'memory search response policy',
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:238:        normalizedQuery: 'memory search response policy',
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:277:      specFolder: 'specs/system-spec-kit/022-hybrid-rag-fusion/filters/fusion-only',
.opencode/skills/system-spec-kit/mcp_server/tests/empty-result-recovery.vitest.ts:360:      specFolder: 'specs/system-spec-kit/022-hybrid-rag-fusion/filters/fusion-only',
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-reindex.ts:2:// MODULE: CocoIndex Re-index Handler
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-reindex.ts:39:            error: 'CocoIndex binary not found. Install: bash .opencode/skills/mcp-coco-index/scripts/install.sh',
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:12:      searchMetadata: {
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:13:        strategy: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:34:      tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:45:    expect(profiled.data.searchMetadata).toEqual({
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:46:      strategy: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:61:  it('preserves metadata fields for research profile', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:62:    const profiled = JSON.parse(applyProfileToEnvelope('research', baseEnvelope, true));
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:66:    expect(profiled.data.searchMetadata).toEqual({
.opencode/skills/system-spec-kit/mcp_server/tests/response-profile-formatters.vitest.ts:67:      strategy: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/validation-metadata.vitest.ts:21:} from '../lib/search/validation-metadata';
.opencode/skills/system-spec-kit/mcp_server/tests/validation-metadata.vitest.ts:22:import type { ValidationMetadata } from '../lib/search/validation-metadata';
.opencode/skills/system-spec-kit/mcp_server/tests/validation-metadata.vitest.ts:23:import type { PipelineRow } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/validation-metadata.vitest.ts:24:import { __testables as stage2Testables } from '../lib/search/pipeline/stage2-fusion';
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:5:// Causal graph search channel — uses FTS5 for node matching
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:7:import { sanitizeFTS5Query } from './bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:12:import type { GraphSearchFn } from './search-types.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:58:// 3. CAUSAL EDGE CHANNEL (FTS5-BACKED)
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:64: * Check whether the FTS5 table exists in the database.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:65: * Used to determine if FTS5 matching is available.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:91: * Uses FTS5 full-text search (memory_fts table) instead of naive LIKE matching.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:92: * Falls back to LIKE only when the FTS5 table is not available.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:103:    // Prefer FTS5 matching for proper full-text search
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:105:      graphResults.push(...queryCausalEdgesFTS5(database, query, limit));
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:107:      // Fallback: LIKE matching when FTS5 table is unavailable
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:144:    console.warn(`[graph-search-fn] Causal edge query failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:150: * FTS5-backed causal edge query. Finds memory IDs via the memory_fts
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:152: * Scores incorporate both edge strength and FTS5 BM25 relevance.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:154:function queryCausalEdgesFTS5(
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:159:  const sanitized = sanitizeFTS5Query(query);
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:163:  // BM25-inspired weights: title(10) highest signal, content(5), triggers(2), folder(1).
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:209:  // Numeric IDs matching memory_index.id (INTEGER column) in the hybrid search
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:256: * Legacy LIKE-based fallback when FTS5 table is unavailable.
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:576:    console.warn('[graph-search-fn] Constitutional exclusion lookup failed; returning zero scores for safety');
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:655: * Creates a graph search function backed by causal_edges only.
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:82:    expect(countStructuralSignals({ title: null, specFolder: '022-hybrid-rag' })).toBe(1);
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:92:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:99:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:122:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:199:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:218:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:228:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:301:      title: 'Decision: adopt FSRS hybrid decay',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:303:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:315:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/short-critical-quality-gate.vitest.ts:329:      specFolder: '022-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/lib/search/validation-metadata.ts:170: * @param row - A PipelineRow as it flows through the search pipeline.
.opencode/skills/system-spec-kit/mcp_server/tests/workflow-memory-tracking.vitest.ts:8:} from '../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/tests/workflow-memory-tracking.vitest.ts:9:import type { PerFolderDescription } from '../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts:4:// MCP tool handler for code_graph_context — LLM-oriented graph neighborhoods.
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts:58:    case 'research':
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts:107:/** Handle code_graph_context tool call */
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts:211:    const profile = (['quick', 'research', 'debug'].includes(args.profile ?? '') ? args.profile : undefined) as ContextArgs['profile'];
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts:274:          error: 'code_graph_context failed',
.opencode/skills/system-spec-kit/mcp_server/tests/incremental-index-v2.vitest.ts:51:        CHECK(context_type IN ('research', 'implementation', 'planning', 'general', 'decision', 'discovery')),
.opencode/skills/system-spec-kit/mcp_server/tests/intent-aware-traversal.vitest.ts:11:} from '../lib/search/causal-boost';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:3:import * as intentClassifier from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:4:import { INTENT_LAMBDA_MAP } from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:5:import type { IntentType, IntentWeights } from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:25:    'fix the broken search bug',
.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:564:describe('T059: autoDetectIntent Parameter (memory_search)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/intent-classifier.vitest.ts:606:        'fix the search not working',
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-surrogates.ts:77:// D2 REQ-D2-005: Query surrogates gate — canonical implementation in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-surrogates.ts:79:import { isQuerySurrogatesEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-surrogates.ts:439: * @param query      - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-state.ts:227:// Session retrieval state gate — canonical implementation in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-state.ts:229:import { isSessionRetrievalStateEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:6:  normalizeContentForBM25,
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:204:      '| Grep | search  | active |',
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:208:    expect(result).toContain('Grep search active');
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:499:// NormalizeContentForBM25
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:500:describe('normalizeContentForBM25', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:502:    expect(normalizeContentForBM25('')).toBe('');
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:507:    const result = normalizeContentForBM25(input);
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:512:    // BM25 pipeline is explicitly identical to embedding at present (per source comments)
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:514:      '---\ntitle: BM25 test\n---',
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:519:    expect(normalizeContentForBM25(input)).toBe(normalizeContentForEmbedding(input));
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:524:    expect(normalizeContentForBM25(input)).not.toContain('title:');
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:525:    expect(normalizeContentForBM25(input)).toContain('Keyword content.');
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:528:  it('S1-B-05: keeps code body for identifier token search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:531:    const result = normalizeContentForBM25(input);
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:538:    expect(normalizeContentForBM25(input)).not.toContain('prettier-ignore');
.opencode/skills/system-spec-kit/mcp_server/tests/content-normalizer.vitest.ts:539:    expect(normalizeContentForBM25(input)).toContain('Searchable token.');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-helpers.vitest.ts:457:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/create-record-lineage-regressions.vitest.ts:5:import { createSchema, ensureSchemaVersion } from '../lib/search/vector-index-schema';
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:274:  describe('T007: Memory filtering removes duplicates from search results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:279:    it('T007: Filters duplicate memories from search results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:282:      const searchResults: MemoryObject[] = [
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:290:      sessionManager.markMemorySent(sessionId, searchResults[1]); // 502
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:291:      sessionManager.markMemorySent(sessionId, searchResults[3]); // 504
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:293:      const { filtered, dedupStats }: FilterResult = sessionManager.filterSearchResults(sessionId, searchResults);
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:339:      const searchResults: MemoryObject[] = [
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:346:      sessionManager.markMemorySent(sessionId, searchResults[0]); // 601
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:347:      sessionManager.markMemorySent(sessionId, searchResults[1]); // 602
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:348:      sessionManager.markMemorySent(sessionId, searchResults[2]); // 603
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:350:      const { filtered, dedupStats }: FilterResult = sessionManager.filterSearchResults(sessionId, searchResults);
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:361:      const searchResults: MemoryObject[] = [
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager.vitest.ts:366:      const { dedupStats: noSavingsStats }: FilterResult = sessionManager.filterSearchResults(sessionId, searchResults);
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:8:import { createSchema, ensureSchemaVersion } from '../lib/search/vector-index-schema';
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:221:    'specs/022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:267:    'specs/022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:281:    'research',
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:297:  `).run(1, 'sess-1', 1, 0.9, now, later, 2, 1, 1, 'memory_search', 'call-1', 'rule-1', 0);
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:312:  `).run('hist-1', 1, null, 'Alpha Memory', 'ADD', now, 0, 'tester', 'specs/022-hybrid-rag-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:325:  `).run(1, later, 'UPDATE', 'hash-beta', 2, 1, 0.82, 'seed conflict', 'beta preview', 'alpha preview', 0, null, 'specs/022-hybrid-rag-fusion', later);
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:358:  `).run(1, 'scope_check', 'allow', 1, 'specs/022-hybrid-rag-fusion::/tmp/specs/022/alpha.md::_', 'tenant-a', 'user-a', 'agent-a', 'sess-1', 'seed governance', '{"phase":"seed"}', later);
.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:364:  `).run('sess-1', 'active', 'specs/022-hybrid-rag-fusion', 'checkpoint test', 'seed', 'summary', '[]', '{"phase":"seed"}', now, later);
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:39:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:49:// Mock hybrid-search
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:50:vi.mock('../lib/search/hybrid-search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:53:    searchWithFallback: mockHybridStage1Search,
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:58:// Mock search-flags
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:64:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:87:vi.mock('../lib/search/embedding-expansion', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:94:vi.mock('../lib/search/query-expander', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:104:vi.mock('../lib/search/llm-reformulation', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:113:vi.mock('../lib/search/hyde', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:122:vi.mock('../lib/search/memory-summaries', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:167:import { executeStage1 } from '../lib/search/pipeline/stage1-candidate-gen';
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:168:import { searchWithFallback } from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:169:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:170:import type { PipelineConfig } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:175:    searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:243:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:267:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:300:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:314:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:344:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:379:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:426:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:478:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:495:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:533:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:548:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:585:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/tests/stage1-expansion.vitest.ts:617:    const mockSearch = searchWithFallback as ReturnType<typeof vi.fn>;
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-feedback.ts:2:// MODULE: CocoIndex Feedback Handler
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-feedback.ts:4:// MCP tool handler for ccc_feedback — accepts search result quality feedback.
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-feedback.ts:45:    const feedbackPath = resolve(projectRoot, '.opencode/skills/mcp-coco-index/feedback/search-feedback.jsonl');
.opencode/skills/system-spec-kit/mcp_server/lib/search/anchor-metadata.ts:8:// Resulting metadata to search pipeline rows. This is a PURE
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:14:import * as hybridSearch from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:746:              title: 'Canonical duplicate from FTS',
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:753:              title: 'Unique FTS entry',
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:784:function canonicalIds(results: Awaited<ReturnType<typeof hybridSearch.hybridSearchEnhanced>>): string[] {
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:785:  return results.map((result) => hybridSearch.__testables.canonicalResultId(result.id));
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:788:describe('T008: includeContent-independent dedup in hybrid search path', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:790:    hybridSearch.init(createHybridMockDb(), mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:791:    hybridSearch.resetGraphMetrics();
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:793:    const results = await hybridSearch.hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:810:    hybridSearch.init(createHybridMockDb(), mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:811:    hybridSearch.resetGraphMetrics();
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:813:    const results = await hybridSearch.hybridSearchEnhanced(
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:831:    hybridSearch.init(createHybridMockDb(), mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:834:    const defaultPath = await hybridSearch.hybridSearchEnhanced('dedup regression query', embedding, {
.opencode/skills/system-spec-kit/mcp_server/tests/content-hash-dedup.vitest.ts:840:    const includeContentPath = await hybridSearch.hybridSearchEnhanced('dedup regression query', embedding, {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-metadata-schema.vitest.ts:136:      || normalized === 'implementation-summary.md' || normalized === 'research.md'
.opencode/skills/system-spec-kit/mcp_server/tests/graph-metadata-schema.vitest.ts:137:      || normalized === 'handover.md' || normalized === 'resource-map.md' || normalized.startsWith('research/')) {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-metadata-schema.vitest.ts:406:    expect(graphMetadataParserTestables.keepKeyFile('research/research.md')).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/dynamic-token-budget.vitest.ts:16:} from '../lib/search/dynamic-token-budget';
.opencode/skills/system-spec-kit/mcp_server/tests/sparse-first-graph.vitest.ts:7:} from '../lib/search/causal-boost';
.opencode/skills/system-spec-kit/mcp_server/tests/sparse-first-graph.vitest.ts:8:import { isTypedTraversalEnabled } from '../lib/search/graph-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/adversarial/README.md:32:  between pre-transaction search and commit; two concurrent conflict
.opencode/skills/system-spec-kit/mcp_server/tests/contradiction-detection.vitest.ts:6:vi.mock('../lib/search/search-flags.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/contradiction-detection.vitest.ts:18:import { isTemporalEdgesEnabled } from '../lib/search/search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-decomposer.ts:71:/** A single candidate pool from one search variant, tagged by query. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-decomposer.ts:94: * @param query - The input search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-decomposer.ts:165: * @param query - The input search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-decomposer.ts:197: * Merge result pools from multiple facet searches, prioritising items that
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:52:import * as intentClassifier from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:83:      { path: '/project/.opencode/specs/003/100-feature/research/research.md', expected: 'research', label: 'research/research.md in specs/' },
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:84:      { path: '/project/.opencode/specs/003/100-feature/research.md', expected: 'research', label: 'legacy research.md in specs/' },
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:130:      expect(types).toContain('research');
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:169:    it('research.md config: semantic, normal, 0.6', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:170:      const config = getSpecDocumentConfig('research' as DocumentType);
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:193:      'decision-record.md', 'implementation-summary.md', 'research.md', 'handover.md', 'resource-map.md', 'description.json',
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:218:      { path: '/p/.opencode/specs/003/100/research/research.md', expected: 'research', label: 'research/research.md' },
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:219:      { path: '/p/.opencode/specs/003/100/research.md', expected: 'research', label: 'legacy research.md' },
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:247:    it('Returns "memory" for iteration files in /research/iterations/', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:248:      expect(extractDocumentType('/p/.opencode/specs/003/100/research/iterations/iteration-001.md')).toBe('memory');
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:370:    it('research -> 0.6', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:371:      expect(calculateDocumentWeight('/p/specs/x/research/research.md', 'research')).toBe(0.6);
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:399:    it('research/review iteration paths fall back to working-artifact weight', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:400:      expect(calculateDocumentWeight('/p/specs/x/research/iterations/iteration-001.md')).toBe(0.25);
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:755:    it('research -> normal', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/full-spec-doc-indexing.vitest.ts:756:      expect(getDefaultTierForDocumentType('research')).toBe('normal');
.opencode/skills/system-spec-kit/mcp_server/tests/retry-manager-health.vitest.ts:13:    vi.doMock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:4:// Feature catalog: BM25 trigger phrase re-index gate
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:6:import { normalizeContentForBM25 } from '../parsing/content-normalizer.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:12:interface BM25SearchResult {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:15:   * BM25 term-frequency relevance score (unbounded, typically 0-25+).
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:22:interface BM25Stats {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:28:interface BM25DocumentSource {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:41:const BM25_WARMUP_BATCH_SIZE = 250;
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:42:const BM25_ENABLED_VALUES = new Set(['1', 'true', 'yes', 'on', 'experimental', 'fallback']);
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:43:const BM25_DISABLED_VALUES = new Set(['0', 'false', 'no', 'off']);
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:46: * C138: Field weight multipliers for weighted BM25 scoring.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:51: * These weights are consumed by the FTS5 path in sqlite-fts.ts,
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:52: * not the in-memory BM25 engine in this file. Exported for shared access.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:59:const BM25_FTS5_WEIGHTS = [10.0, 5.0, 2.0, 1.0] as const;
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:61:const BM25_FIELD_WEIGHTS: Record<string, number> = {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:62:  title: BM25_FTS5_WEIGHTS[0],
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:63:  trigger_phrases: BM25_FTS5_WEIGHTS[1],
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:64:  content_generic: BM25_FTS5_WEIGHTS[2],
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:65:  body: BM25_FTS5_WEIGHTS[3],
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:69: * Check whether the in-memory BM25 index is enabled.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:71: * @returns `true` when BM25 indexing/search is enabled for the current process.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:80:  const value = process.env.ENABLE_BM25?.trim().toLowerCase();
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:82:  if (BM25_DISABLED_VALUES.has(value)) return false;
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:83:  return BM25_ENABLED_VALUES.has(value);
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:99: * Apply lightweight stemming to a token for BM25 indexing and matching.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:146: * Tokenize raw text into normalized BM25 terms.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:163: * Count token frequency occurrences for BM25 scoring.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:169: * getTermFrequencies(['memory', 'memory', 'search']).get('memory');
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:181:function normalizeTriggerPhrasesForBM25(triggerPhrases: string | string[] | null | undefined): string {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:211:function buildBm25DocumentText(row: BM25DocumentSource): string {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:219:    textParts.push(normalizeContentForBM25(row.content_text));
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:222:  const triggerPhrases = normalizeTriggerPhrasesForBM25(row.trigger_phrases);
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:235:// 3. BM25 INDEX CLASS
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:238:class BM25Index {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:322:  search(query: string, limit: number = 10): BM25SearchResult[] {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:326:    const results: BM25SearchResult[] = [];
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:340:  getStats(): BM25Stats {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:414:      console.warn(`[bm25-index] Failed to sync BM25 rows: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:444:        const batchIds = pendingIds.splice(0, BM25_WARMUP_BATCH_SIZE);
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:463:      console.warn(`[bm25-index] Failed to schedule BM25 warmup: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:481:let indexInstance: BM25Index | null = null;
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:484: * Retrieve the shared in-memory BM25 index singleton.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:486: * @returns The process-wide {@link BM25Index} instance.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:490: * index.addDocument('123', 'memory search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:493:function getIndex(): BM25Index {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:495:    indexInstance = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:501: * Reset the shared BM25 index singleton.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:515:// 5. FTS5 QUERY SANITIZATION (P3-06)
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:519: * Sanitize a query string for safe use with SQLite FTS5 and return
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:521: * entry point — both FTS5 query construction and BM25 callers should
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:524: * Removes all FTS5 operators and special characters, then returns
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:527: * @param query - Raw user query text that may contain FTS operators.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:528: * @returns Sanitized query tokens safe to reuse for lexical search paths.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:540:  // Remove FTS5 boolean/proximity operators (case-insensitive)
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:548:  // Remove FTS5 special characters and column-filter colon.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:579: * Sanitize a query string for safe use with SQLite FTS5.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:581: * each token in quotes for FTS5 safety.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:584: * @returns A quoted FTS5-safe query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:587: * sanitizeFTS5Query('memory search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:588: * // "\"memory\" \"search\""
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:591:function sanitizeFTS5Query(query: string): string {
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:602:  BM25Index,
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:610:  sanitizeFTS5Query,
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:615:  BM25_FTS5_WEIGHTS,
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:616:  BM25_FIELD_WEIGHTS,
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:620:  BM25SearchResult,
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:621:  BM25Stats,
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:622:  BM25DocumentSource,
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:13:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:18:import { searchCommunities } from '../lib/search/community-search';
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:53:describe('searchCommunities()', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:68:      { id: 1, summary: 'search retrieval pipeline', memberIds: [1, 2], count: 2 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:71:    expect(searchCommunities('search', db)).toEqual({
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:79:    expect(searchCommunities('search', db)).toEqual({
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:88:      { id: 1, summary: 'vector embeddings and search', memberIds: [1, 2], count: 2 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:89:      { id: 2, summary: 'graph retrieval search quality', memberIds: [3, 4, 5], count: 3 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:93:    const result = searchCommunities('search quality', db);
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:109:      { id: 1, summary: 'search one', memberIds: [1], count: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:110:      { id: 2, summary: 'search two', memberIds: [2], count: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:111:      { id: 3, summary: 'search three', memberIds: [3], count: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:114:    const result = searchCommunities('search', db, 2);
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:122:      { id: 1, summary: 'search pipeline alpha', memberIds: [1, 2, 3], count: 3 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:123:      { id: 2, summary: 'search pipeline beta', memberIds: [2, 3, 4], count: 3 },
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts:126:    const result = searchCommunities('search pipeline', db);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-flags.vitest.ts:6:import { isGraphUnifiedEnabled } from '../lib/search/graph-flags';
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-status.ts:2:// MODULE: CocoIndex Status Handler
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-status.ts:4:// MCP tool handler for ccc_status — reports CocoIndex availability and stats.
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-status.ts:55:              ? 'Install CocoIndex: bash .opencode/skills/mcp-coco-index/scripts/install.sh'
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-status.ts:58:                : 'CocoIndex is ready. Use mcp__cocoindex_code__search for semantic queries.',
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:2:// Converted from: search-extended.test.ts (custom runner)
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:9:} from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:19:} from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:31:  delete process.env.ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:37:  for (const key of ['VOYAGE_API_KEY', 'COHERE_API_KEY', 'RERANKER_LOCAL', 'ENABLE_BM25']) {
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:49:   A. BM25-INDEX: simpleStem
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:104:   B. BM25-INDEX: isBm25Enabled
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:112:  it('BM01: returns true when ENABLE_BM25 not set (BM25 is enabled by default)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:113:    delete process.env.ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:118:  it('BM02: returns false when ENABLE_BM25=false', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:119:    process.env.ENABLE_BM25 = 'false';
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:123:  it('BM03: returns true when ENABLE_BM25=true', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:124:    process.env.ENABLE_BM25 = 'true';
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:128:  it('BM04: returns false for ENABLE_BM25=0 (non-truthy values stay disabled)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:129:    process.env.ENABLE_BM25 = '0';
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:135:   C. BM25-INDEX: DEFAULT_K1 and DEFAULT_B constants
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:144:  it('K1-02: DEFAULT_K1 in typical BM25 range [0.5, 3.0]', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts:158:  it('B-02: DEFAULT_B in typical BM25 range [0, 1.0]', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/importance-tiers.vitest.ts:8:// Comparison, and decay/search behavior per tier.
.opencode/skills/system-spec-kit/mcp_server/tests/importance-tiers.vitest.ts:64:        expect(config.searchBoost).toBe(expectedBoost);
.opencode/skills/system-spec-kit/mcp_server/lib/search/spec-folder-hierarchy.ts:7:// Parses folder paths like "system-spec-kit/140-hybrid-rag/006-sprint-5"
.opencode/skills/system-spec-kit/mcp_server/lib/search/spec-folder-hierarchy.ts:75: * Parses folder paths like "system-spec-kit/140-hybrid-rag/006-sprint-5"
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:20:} from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:36:import { resolveGraphWalkRolloutState } from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:50:} from '../lib/search/dynamic-token-budget';
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:58: * used by graph-search-fn.ts (computeTypedDegree, computeMaxTypedDegree,
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:268:      { source: SOURCE_TYPES.FTS, results: [{ id: 2 }, { id: 3 }] },
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:269:      { source: SOURCE_TYPES.BM25, results: [{ id: 3 }, { id: 1 }] },
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:337:    // Build the degree ranked list as hybrid-search would
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:20:import { executePipeline } from '../lib/search/pipeline/index.js';
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:33:vi.mock('../lib/search/pipeline/index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:43:vi.mock('../lib/search/session-boost.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:47:vi.mock('../lib/search/causal-boost.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:92:    ) VALUES (?, 'search', ?, 2, ?)
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:186:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:304:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:339:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:376:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:428:        searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:473:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:508:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:543:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-evaluation-runtime.vitest.ts:586:      searchLimit: 5,
.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:7:// search result, composed from the scoring signals applied during
.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:75:import { isResultExplainEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:98:  // Lexical match: only present if the row came through FTS channel
.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:268:  const hasFTS = channelAttribution.includes('fts') || channelAttribution.includes('bm25');
.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:271:  if (hasFTS && hasGraph) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:281:  if (hasFTS) {
.opencode/skills/system-spec-kit/mcp_server/tests/p0-d-toctou-cleanup-regression.vitest.ts:61:      lastSpecFolder: 'specs/system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-index-cooldown.vitest.ts:93:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/ground-truth.vitest.ts:639:    expect(q!.query).toBe('what does maxTriggersPerMemory control in the search pipeline');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:4:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:60:    path.join(SERVER_DIR, 'configs', 'search-weights.json'),
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:61:    path.join(SERVER_DIR, '..', 'configs', 'search-weights.json'),
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:73:let _search_weights: SearchWeightsConfig | null = null;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:76:  if (_search_weights === null) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:77:    _search_weights = loadSearchWeights();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:79:  return _search_weights;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:82:/** Loaded search weight configuration for vector-index ranking (lazy-loaded). */
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:83:export const search_weights: SearchWeightsConfig = {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:250:        `but the active embedding configuration resolves to ${current_dim}. Refusing to bootstrap because vector search would fail. ` +
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:796:    console.warn('[vector-index] Falling back to anchor-only mode (no vector search)');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:873:// Check if vector search is available (sqlite-vec loaded)
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:875: * Reports whether sqlite-vec vector search is available.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:876: * @returns True when vector search is available.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:878:export function is_vector_search_available(): boolean {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:910:   * @param embedding - The query embedding to search with.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:917:   * const rows = await store.search(queryEmbedding, 10, { specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:920:  async search(embedding: EmbeddingInput, topK: number, options: VectorSearchOptions = {}): Promise<MemoryRow[]> {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:932:    const search_options = {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:943:    const { vector_search } = await getQueriesModule();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:944:    return vector_search(embedding, search_options, database);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:1076:  async searchEnriched(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:1082:    const { vector_search_enriched } = await getQueriesModule();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:1083:    return vector_search_enriched(embedding, undefined, options, database);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:1089:    const { enhanced_search } = await getAliasesModule();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:1090:    return enhanced_search(embedding, undefined, options, database);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:1135:export { is_vector_search_available as isVectorSearchAvailable };
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts:9:// Seeds are retrieved via a lightweight keyword-only search using
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts:10:// BM25/FTS5 (no embedding call) to ground the LLM prompt in real
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts:79:// D2 REQ-D2-003: LLM reformulation gate — canonical implementation in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts:81:import { isLlmReformulationEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts:91: * Uses FTS5 / BM25 keyword search only — no embedding call — to keep
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts:98: * @param query - The raw search query to ground against.
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts:157:    'You are a search query reformulation assistant.',
.opencode/skills/system-spec-kit/mcp_server/tests/learning-stats-filters.vitest.ts:5:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:9:} from '../lib/search/artifact-routing';
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:10:import type { ArtifactClass, RetrievalStrategy, WeightedResult } from '../lib/search/artifact-routing';
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:46:  it('classifies research.md files', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:47:    expect(classifyArtifact('/specs/007-auth/research/research.md')).toBe('research');
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:48:    expect(classifyArtifact('/specs/007-auth/research.md')).toBe('research');
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:81:      'decision-record', 'implementation-summary', 'memory', 'research',
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:122:  it('verifies checklist strategy favors keyword search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/artifact-routing.vitest.ts:282:      'memory', 'research', 'unknown',
.opencode/skills/system-spec-kit/mcp_server/tests/hooks-mutation-wiring.vitest.ts:40:vi.mock('../lib/search/graph-search-fn', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:24:} from '../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:25:import type { FolderDescription, DescriptionCache, PerFolderDescription } from '../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:33:    const content = `# Hybrid RAG Fusion Refinement\n\nThis spec describes the hybrid approach.`;
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:111:    expect(keywords).toContain('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:135:    const keywords = extractKeywords('memory memory memory search search');
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:137:    const searchCount = keywords.filter(k => k === 'search').length;
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:139:    expect(searchCount).toBe(1);
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:143:    const keywords = extractKeywords('BM25 Vector Hybrid SEARCH');
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:146:    expect(keywords).toContain('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:147:    expect(keywords).toContain('search');
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:182:        description: 'Semantic memory search with vector embeddings and BM25 index',
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:183:        keywords: ['semantic', 'memory', 'search', 'vector', 'embeddings', 'bm25', 'index'],
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:187:        specFolder: 'specs/003-hybrid-rag',
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:189:        keywords: ['hybrid', 'rag', 'fusion', 'pipeline', 'combining', 'vector', 'keyword', 'retrieval'],
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:202:    const results = findRelevantFolders('vector search memory', mockCache);
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:204:    // Specs/002-memory should score highly — has 'vector', 'memory', 'search'
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:211:    const results = findRelevantFolders('hybrid rag fusion vector', mockCache);
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:226:    const results = findRelevantFolders('vector search routing', mockCache, 2);
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:237:    const results = findRelevantFolders('memory search', mockCache);
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery.vitest.ts:250:    expect(findRelevantFolders('memory search', emptyCache)).toEqual([]);
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposition.vitest.ts:5:import { __testables } from '../lib/search/pipeline/stage1-candidate-gen';
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposition.vitest.ts:6:import type { PipelineRow } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/concept-routing.vitest.ts:8:} from '../lib/search/entity-linker';
.opencode/skills/system-spec-kit/mcp_server/tests/concept-routing.vitest.ts:61:    const tokens = nounPhrases('memory-search: find embeddings!');
.opencode/skills/system-spec-kit/mcp_server/tests/concept-routing.vitest.ts:222:    const { isGraphConceptRoutingEnabled } = await import('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/concept-routing.vitest.ts:228:    const { isGraphConceptRoutingEnabled } = await import('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/concept-routing.vitest.ts:234:    const { isGraphConceptRoutingEnabled } = await import('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/concept-routing.vitest.ts:240:    const result = routeQueryConcepts('memory retrieval pipeline search');
.opencode/skills/system-spec-kit/mcp_server/tests/k-value-judged-sweep.vitest.ts:254:        { source: SOURCE_TYPES.BM25,   results: results2 },
.opencode/skills/system-spec-kit/mcp_server/tests/d5-confidence-scoring.vitest.ts:13:} from '../lib/search/confidence-scoring';
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:6:// Learning from selections, and enhanced search with ranking+diversity.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:16:  search_weights,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:19:  vector_search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:20:  vector_search_enriched,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:43:  searchMethod?: string;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:54:const MAX_TRIGGERS_PER_MEMORY = search_weights.maxTriggersPerMemory || 10;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:69:/** Maintains a TTL-based least-recently-used cache for search helpers. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:187: * Builds a stable cache key for a search request.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:188: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:190: * @param options - Additional search options.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:199:// Cached version of vector_search_enriched with LRU cache
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:201: * Runs an enriched search with LRU caching.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:202: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:204: * @param options - Additional search options.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:205: * @returns The enriched search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:207:export async function cached_search(query: string, limit = 20, options: Record<string, unknown> = {}): Promise<EnrichedSearchResult[]> {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:219:  const results = await vector_search_enriched(query, limit, options);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:227: * Clears cached search results globally or for one spec folder.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:231:export function clear_search_cache(spec_folder: string | null = null): number {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:261: * @param search_query - The original search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:265:export function learn_from_selection(search_query: string, selected_memory_id: number): boolean {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:266:  if (!search_query || !selected_memory_id) return false;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:296:  const new_terms = search_query
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:346:    const similar = vector_search(embedding, {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:399: * Runs enriched search with smart ranking and diversity controls.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:400: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:403: * @returns The ranked search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:405:export async function enhanced_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:415:  const results = await vector_search_enriched(query, fetch_limit, {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:429:    console.warn(`[vector-index] Enhanced search took ${elapsed}ms (target <600ms)`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:436:export { cached_search as cachedSearch };
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:437:export { clear_search_cache as clearSearchCache };
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:441:export { enhanced_search as enhancedSearch };
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-router.ts:48:const BM25_PRESERVING_ARTIFACTS = new Set([
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-router.ts:55:  'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-router.ts:120:  return BM25_PRESERVING_ARTIFACTS.has(artifact);
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-router.ts:134: * @param query - The search query to classify and route
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/gold-query-verifier.ts:18: * Canonical on-disk path to the v1 gold battery shipped under the 007 research
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/gold-query-verifier.ts:21: * REQ-014: keep in sync if the asset moves under the 007 research packet.
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/gold-query-verifier.ts:24:  '../../../../../specs/system-spec-kit/026-graph-and-context-optimization/005-code-graph/006-code-graph-resilience-research/assets/code-graph-gold-queries.json',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-crud.vitest.ts:6:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:7:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:22:} from '../lib/search/embedding-expansion';
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:51:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:55:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:77:    // Default: vector search returns nothing (safe baseline)
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:95:    // Vector search must NOT be called when the flag is off
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:121:    // Vector search must NOT run for simple queries
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:148:      makeMockMemory(2, 'embedding similarity vector search semantic expansion candidates'),
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:149:      makeMockMemory(3, 'hybrid retrieval fusion recall semantic candidates'),
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:155:    // Vector search must have been called once
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:190:    // Vector search should have been called (expansion attempted)
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:316:  it('T11: combinedQuery === original when vector search returns no content', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:320:    // Vector search returns memories without content fields
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:345:        title: 'architecture retrieval deep search',
.opencode/skills/system-spec-kit/mcp_server/tests/embedding-expansion.vitest.ts:352:    const query = 'semantic pipeline query expansion complex architecture retrieval deep search';
.opencode/skills/system-spec-kit/mcp_server/tests/context-server-error-envelope.vitest.ts:9:    const response = buildErrorResponse('memory_search', err, { input: 'test' });
.opencode/skills/system-spec-kit/mcp_server/tests/context-server-error-envelope.vitest.ts:23:    const errorResponse = buildErrorResponse('memory_context', err, {});
.opencode/skills/system-spec-kit/mcp_server/lib/search/channel-representation.ts:14:import { isChannelMinRepEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/thin-continuity-record.vitest.ts:40:        'research//iterations/iteration-024.md',
.opencode/skills/system-spec-kit/mcp_server/tests/thin-continuity-record.vitest.ts:67:      key_files: ['research/iterations/iteration-024.md', 'scratch/resource-map/04-templates.md'],
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:16:import { computeDegreeScores } from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:17:import { recomputeLocal } from '../lib/search/graph-lifecycle';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:18:import { delete_memory_from_database } from '../lib/search/vector-index-mutations';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:798:  describe('search and degree performance regressions', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:837:    it('uses CTE-based FTS edge lookup and caches FTS table availability per DB', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:869:      const graphSearchModule = await import('../lib/search/graph-search-fn');
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:876:      const search = (createSearchFn as (database: Database.Database) => (query: string, options: Record<string, unknown>) => Array<Record<string, unknown>>)(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:877:      const first = search('authentication', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/graph-signals.vitest.ts:878:      const second = search('authentication', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/query-router.vitest.ts:21:} from '../lib/search/query-router';
.opencode/skills/system-spec-kit/mcp_server/tests/query-router.vitest.ts:70:  'memory search',
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:9:} from '../lib/search/query-decomposer';
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:10:import type { FacetPool } from '../lib/search/query-decomposer';
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:49:    expect(isMultiFacet('find embedding results or return graph search candidates')).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:65:    expect(isMultiFacet('Explain the hybrid search. Describe the scoring algorithm.')).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:73:    expect(isMultiFacet('describe the hybrid search pipeline scoring approach')).toBe(false);
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:95:    const facets = decompose('return embedding results or return graph search candidates');
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:113:    const facets = decompose('search for memories and search for memories in deep mode');
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:120:    const facets = decompose('Explain the hybrid search pipeline. Describe the scoring algorithm.');
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:254:    const { isQueryDecompositionEnabled } = await import('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/query-decomposer.vitest.ts:261:    const { isQueryDecompositionEnabled } = await import('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-expander.ts:51:  search: ['retrieval', 'query'],
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-expander.ts:63: * Expand a query into multiple search variants using synonym maps.
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-expander.ts:70: * @param query - The input search query string.
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:10:// 2. specFolder forwarded in Stage 1 — hybrid channel
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:15:// 7. structuralSearch (hybrid fallback Tier 3) respects specFolder
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:29:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:40:// Capture call arguments for the Stage 1 hybrid raw-collector path.
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:44:vi.mock('../lib/search/hybrid-search', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:45:  const actual = await importOriginal<typeof import('../lib/search/hybrid-search')>();
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:52:    searchWithFallback: mockStage1HybridSearch,
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:61:// BM25 — prevent filesystem access during hybrid-search init
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:62:vi.mock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:64:    search: vi.fn(() => []),
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:67:  sanitizeFTS5Query: vi.fn((q: string) => q),
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:71:vi.mock('../lib/search/sqlite-fts', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:76:vi.mock('../lib/search/query-expander', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:81:vi.mock('../lib/search/embedding-expansion', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:87:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:105:import { executeStage1 } from '../lib/search/pipeline/stage1-candidate-gen';
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:106:import type { Stage1Input, PipelineConfig } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:107:import { structuralSearch, init } from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:117:    searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:206:        searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:224:        searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:240:// 2. Stage 1 — specFolder forwarded to hybrid channel
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:243:describe('R9: Stage 1 spec-folder forwarding — hybrid channel', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:246:  it('R9-03: searchWithFallback is called with specFolder when provided', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:249:        searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:263:  it('R9-04: searchWithFallback is called with no specFolder when not provided', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:266:        searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:290:        searchType: 'multi-concept',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:291:        concepts: ['hybrid RAG', 'vector search'],
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:308:        searchType: 'multi-concept',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:325:        searchType: 'multi-concept',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:348:        searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:378:        searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:392:  it('R9-09: no specFolder means no folder filter in searchWithFallback options', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:395:        searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:412:        searchType: 'multi-concept',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:439:        searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:453:  it('R9-11: returns empty candidates when searchWithFallback returns [] for non-existent specFolder', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:456:        searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:472:        searchType: 'multi-concept',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:488:// 7. structuralSearch (hybrid fallback Tier 3) — real DB tests
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:558:        searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:568:        searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:576:  it('R9-18: metadata.searchType reflects the configured search channel', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:577:    for (const searchType of ['vector', 'hybrid'] as const) {
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:580:        config: makePipelineConfig({ searchType }),
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:582:      expect(output.metadata.searchType).toBe(searchType);
.opencode/skills/system-spec-kit/mcp_server/tests/spec-folder-prefilter.vitest.ts:588:      config: makePipelineConfig({ searchType: 'vector' }),
.opencode/skills/system-spec-kit/mcp_server/tests/remediation-008-docs.vitest.ts:14:describe('008 search fusion and reranker remediation docs', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/remediation-008-docs.vitest.ts:17:      '.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-skill-graph-metadata-routing-boosts/008-deep-skill-feature-catalogs/spec.md',
.opencode/skills/system-spec-kit/mcp_server/tests/remediation-008-docs.vitest.ts:20:    expect(spec).toContain('sk-deep-research/feature_catalog/` -- root catalog + 14 feature entries across 4 categories');
.opencode/skills/system-spec-kit/mcp_server/tests/remediation-008-docs.vitest.ts:27:      '.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/004-smart-router-context-efficacy/001-initial-research/research/research-validation.md',
.opencode/skills/system-spec-kit/mcp_server/tests/graph-lifecycle.vitest.ts:27:} from '../lib/search/graph-lifecycle';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-lifecycle.vitest.ts:35:} from '../lib/search/graph-lifecycle';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-lifecycle.vitest.ts:550:    expect(subject.toLowerCase()).toContain('graphsearch');
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts:7:import * as crossEncoder from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts:12:} from '../lib/search/graph-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts:25:} from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts:232:} from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts:275:  it('resolveSavePlannerMode accepts hybrid', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts:276:    process.env.SPECKIT_SAVE_PLANNER_MODE = 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts:277:    expect(resolveSavePlannerMode()).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/mpab-quality-gate-integration.vitest.ts:47:// Feature flags from search-flags
.opencode/skills/system-spec-kit/mcp_server/tests/mpab-quality-gate-integration.vitest.ts:52:} from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:18:} from '../lib/search/query-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:26:  'memory search',
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:33:  'search tools',
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:43:  'search memory',
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:46:  'memory search',           // Trigger match
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:64:  'optimize the search query performance',
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:76:  'investigate why the search results are returning duplicate entries when using the advanced filter with pagination',
.opencode/skills/system-spec-kit/mcp_server/tests/query-classifier.vitest.ts:197:      const result = classifyQueryComplexity('search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:414:// V14: Add content_text column + FTS5 rebuild for BM25 full-text search across restarts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:782:        logger.info('Migration v14: Rebuilt FTS5 table with content_text');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:784:        console.warn('[VectorIndex] Migration v14 warning (FTS5 rebuild):', get_error_message(e));
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1178:      if (tableInfo?.sql && !tableInfo.sql.includes("context_type IN ('research', 'implementation', 'planning', 'general')")) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1197:          "CHECK(context_type IN ('research', 'implementation', 'planning', 'general'))"
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1203:            "context_type TEXT DEFAULT 'general' CHECK(context_type IN ('research', 'implementation', 'planning', 'general'))"
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2385:      context_type TEXT DEFAULT 'general' CHECK(context_type IN ('research', 'implementation', 'planning', 'general')),
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2443:  // Create FTS5 virtual table (includes content_text for full-text search)
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2451:  // Create FTS5 sync triggers (includes content_text)
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:9:  hybridAdaptiveFuse,
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:133:    for (const docType of ['decision', 'implementation', 'research']) {
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:161:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:177:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:196:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:212:    const outOfBucket = hybridAdaptiveFuse(semantic, keyword, 'understand', { identity: 'session-0' });
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:213:    const inBucket = hybridAdaptiveFuse(semantic, keyword, 'understand', { identity: 'session-3' });
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:227:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand', { darkRun: true });
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:240:  it('T12: degraded contract is assembled by hybridAdaptiveFuse when adaptive fusion throws', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:265:    const result = dynamicFusion.hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:282:    const result = hybridAdaptiveFuse([], [], 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:316:    it('C138-T1: find_spec intent heavily weights FTS5/keyword', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:329:    it('C138-T3: hybridAdaptiveFuse produces different rankings per intent', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:334:      const understandResult = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fusion.vitest.ts:335:      const fixBugResult = hybridAdaptiveFuse(semantic, keyword, 'fix_bug');
.opencode/skills/system-spec-kit/mcp_server/tests/safety.vitest.ts:115:            CHECK(context_type IN ('research', 'implementation', 'planning', 'general', 'decision', 'discovery')),
.opencode/skills/system-spec-kit/mcp_server/tests/flag-ceiling.vitest.ts:28:} from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/flag-ceiling.vitest.ts:31: * All SPECKIT_* feature flags from search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/tests/flag-ceiling.vitest.ts:200:// Verified: All 20 SPECKIT_* flags from search-flags.ts covered
.opencode/skills/system-spec-kit/mcp_server/tests/channel-representation.vitest.ts:14:} from '../lib/search/channel-representation';
.opencode/skills/system-spec-kit/mcp_server/tests/channel-representation.vitest.ts:212:      ['bm25',   [makeChannelResult('b1', 0.55, { title: 'BM25 Doc' })]],
.opencode/skills/system-spec-kit/mcp_server/tests/channel-representation.vitest.ts:223:    expect((p as Record<string, unknown>).title).toBe('BM25 Doc'); // extra fields preserved
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:1:// TEST: BM25 SECURITY
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:5:  BM25Index,
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:6:  sanitizeFTS5Query,
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:11:} from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:38:      throw new Error(`Unexpected SQL in BM25 rebuild test: ${sql}`);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:43:describe('BM25 Security & Coverage Gap Tests', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:45:     sanitizeFTS5Query: Basic Passthrough
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:48:  describe('sanitizeFTS5Query: Basic Passthrough', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:50:      expect(sanitizeFTS5Query('memory')).toBe('"memory"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:54:      expect(sanitizeFTS5Query('memory search retrieval')).toBe('"memory" "search" "retrieval"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:58:      expect(sanitizeFTS5Query('real-time')).toBe('"real-time"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:62:      expect(sanitizeFTS5Query('memory_index')).toBe('"memory_index"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:66:      expect(sanitizeFTS5Query('version 42')).toBe('"version" "42"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:71:     sanitizeFTS5Query: SQL Injection Attempts
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:74:  describe('sanitizeFTS5Query: SQL Injection Attempts', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:76:      const result = sanitizeFTS5Query("'; DROP TABLE memory_index; --");
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:84:      const result = sanitizeFTS5Query("1 UNION SELECT * FROM sqlite_master");
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:91:      const result = sanitizeFTS5Query("search -- comment injection");
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:92:      expect(result).toContain('"search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:97:      const result = sanitizeFTS5Query("test; DELETE FROM memory_index WHERE 1=1;");
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:103:     sanitizeFTS5Query: FTS5 Operator Removal
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:106:  describe('sanitizeFTS5Query: FTS5 Operator Removal', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:108:      expect(sanitizeFTS5Query('memory AND search')).toBe('"memory" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:112:      expect(sanitizeFTS5Query('memory OR search')).toBe('"memory" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:116:      expect(sanitizeFTS5Query('memory NOT deleted')).toBe('"memory" "deleted"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:120:      expect(sanitizeFTS5Query('memory NEAR search')).toBe('"memory" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:124:      const result = sanitizeFTS5Query('memory NEAR/3 search');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:126:      expect(result).toContain('"search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:131:      const result = sanitizeFTS5Query('memory And search Or retrieval Not deleted near context');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:137:      expect(result).toContain('"search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:144:      const result = sanitizeFTS5Query('memory and search or retrieval not deleted near context');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:152:      expect(sanitizeFTS5Query('android')).toBe('"android"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:153:      expect(sanitizeFTS5Query('fortune')).toBe('"fortune"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:154:      expect(sanitizeFTS5Query('notable')).toBe('"notable"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:155:      expect(sanitizeFTS5Query('nearby')).toBe('"nearby"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:160:     sanitizeFTS5Query: Special Character Handling
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:163:  describe('sanitizeFTS5Query: Special Character Handling', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:165:      expect(sanitizeFTS5Query('mem* search')).toBe('"mem" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:169:      expect(sanitizeFTS5Query('^memory search')).toBe('"memory" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:173:      expect(sanitizeFTS5Query('(memory search)')).toBe('"memory" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:177:      expect(sanitizeFTS5Query('{memory}')).toBe('"memory"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:181:      expect(sanitizeFTS5Query('[memory]')).toBe('"memory"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:185:      expect(sanitizeFTS5Query('"exact phrase"')).toBe('"exact" "phrase"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:189:      expect(sanitizeFTS5Query('title:memory')).toBe('"title" "memory"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:193:      expect(sanitizeFTS5Query('col1:val1 col2:val2')).toBe('"col1" "val1" "col2" "val2"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:196:    it('S26: Non-FTS5 special chars preserved', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:197:      expect(sanitizeFTS5Query('!alert @user #tag $var %mod &ref')).toBe('"!alert" "@user" "#tag" "$var" "%mod" "&ref"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:200:    it('S27: All FTS5 specials removed at once', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:201:      expect(sanitizeFTS5Query('*^(){}[]":test')).toBe('"test"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:206:     sanitizeFTS5Query: Whitespace & Empty Input
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:209:  describe('sanitizeFTS5Query: Whitespace & Empty Input', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:211:      expect(sanitizeFTS5Query('')).toBe('');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:215:      expect(sanitizeFTS5Query('   ')).toBe('');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:219:      expect(sanitizeFTS5Query('  memory  ')).toBe('"memory"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:223:      expect(sanitizeFTS5Query('memory    search     retrieval')).toBe('"memory" "search" "retrieval"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:227:      expect(sanitizeFTS5Query('memory\tsearch')).toBe('"memory" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:231:      expect(sanitizeFTS5Query('memory\nsearch\nretrieval')).toBe('"memory" "search" "retrieval"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:235:      expect(sanitizeFTS5Query('AND OR NOT NEAR')).toBe('');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:239:      expect(sanitizeFTS5Query('*^(){}[]"')).toBe('');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:244:     sanitizeFTS5Query: Unicode & Encoding
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:247:  describe('sanitizeFTS5Query: Unicode & Encoding', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:249:      // Input is NFD (decomposed); sanitizeFTS5Query preserves encoding as-is
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:250:      expect(sanitizeFTS5Query('cafe\u0301 re\u0301sume\u0301')).toBe('"cafe\u0301" "re\u0301sume\u0301"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:254:      expect(sanitizeFTS5Query('\u30e1\u30e2\u30ea \u691c\u7d22')).toBe('"\u30e1\u30e2\u30ea" "\u691c\u7d22"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:258:      expect(sanitizeFTS5Query('\ud83d\udd0d search')).toBe('"\ud83d\udd0d" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:262:      const result = sanitizeFTS5Query('hello\x00world');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:269:     sanitizeFTS5Query: Complex Attack Vectors
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:272:  describe('sanitizeFTS5Query: Complex Attack Vectors', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:274:      const result = sanitizeFTS5Query('test" OR "1"="1');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:280:      expect(sanitizeFTS5Query('content:memory OR title:admin')).toBe('"content" "memory" "title" "admin"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:284:      expect(sanitizeFTS5Query('mem*')).toBe('"mem"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:289:      const result = sanitizeFTS5Query(longInput);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:299:      const result = sanitizeFTS5Query('(memory AND search*) OR NOT "title":admin NEAR/5 secret');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:301:      expect(result).toContain('"search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:311:      expect(sanitizeFTS5Query('path\\to\\file')).toBe('"path\\to\\file"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:315:      const result = sanitizeFTS5Query('hello world test');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:322:      expect(sanitizeFTS5Query('OR x')).toBe('"x"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:326:      expect(sanitizeFTS5Query('NOT memory AND search OR')).toBe('"memory" "search"');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:347:      const freq = getTermFrequencies(['memory', 'search', 'memory', 'memory', 'search']);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:349:      expect(freq.get('search')).toBe(2);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:370:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:379:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:392:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:394:        { id: 1, title: 'Memory System', content_text: 'Semantic search retrieval', trigger_phrases: 'memory,search', file_path: 'specs/001/spec.md' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:395:        { id: 2, title: 'Index Management', content_text: 'BM25 indexing pipeline', trigger_phrases: 'index,bm25', file_path: 'specs/002/spec.md' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:413:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:434:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:456:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:483:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:489:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:497:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:498:      index.addDocument('idf1', 'memory search retrieval testing');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:506:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:507:      index.addDocument('score1', 'memory search retrieval testing context');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:514:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-causal-graph.vitest.ts:53:    { id: 204, filePath: 'research.md', title: 'Research' },
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-causal-graph.vitest.ts:116:      targetAnchor: 'research#research-anchor',
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-causal-graph.vitest.ts:117:      evidence: 'Checklist anchor contradicts research anchor',
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-causal-graph.vitest.ts:123:      sourceAnchor: 'research#research-anchor',
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-causal-graph.vitest.ts:125:      evidence: 'Research anchor derives the spec anchor',
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:20:  generateCacheKey: vi.fn(() => 'gate-d-benchmark-memory-search'),
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:27:vi.mock('../lib/search/pipeline', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:54:      stage1: { searchType: 'hybrid', channelCount: 3, candidateCount: 3, constitutionalInjected: 0, durationMs: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:79:    _searchType: string,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:108:vi.mock('../lib/search/artifact-routing', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:113:vi.mock('../lib/search/intent-classifier', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:145:import { handleMemorySearch } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:161:describe('Gate D benchmark — memory search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:170:  it('keeps canonical memory-search across 7 intents under the Gate D latency budget', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:174:    for (const searchCase of SEARCH_QUERIES) {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:178:          query: searchCase.query,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:179:          intent: searchCase.intent,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts:193:    console.log(`[gate-d-benchmark][search] p50=${summary.p50.toFixed(2)}ms p95=${summary.p95.toFixed(2)}ms p99=${summary.p99.toFixed(2)}ms samples=${durations.length}`);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:3:import { __testables, truncateToBudget, estimateResultTokens } from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:18:      source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:44:      source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:45:      file_path: '/workspace/.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/019-sprint-9-extra-features/implementation-summary.md',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:50:      ['022-hybrid-rag-fusion/019-sprint-9-extra-features', 'Description'],
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:63:        source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:70:        source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:77:        source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:111:        source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:118:        source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:150:      source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:171:      source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts:190:      source: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:3:description: "5-channel hybrid search architecture combining vector, lexical (BM25/FTS5), graph-based and structure-aware graph retrieval with Reciprocal Rank Fusion (RRF) and Adaptive Fusion."
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:5:  - "search subsystem"
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:6:  - "hybrid search"
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:7:  - "vector search"
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:12:> 5-channel hybrid search architecture combining vector, lexical (BM25/FTS5), graph-based and structure-aware graph retrieval, fused with Reciprocal Rank Fusion (RRF) and Adaptive Fusion.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:27:- [FTS CAPABILITY CASCADE FLOOR](#fts-capability-cascade-floor)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:39:The search subsystem provides production-grade hybrid search capabilities with multiple retrieval methods fused via RRF scoring. It handles query expansion, intent classification, typo tolerance and optional cross-encoder reranking.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:44:- **5-Channel Hybrid Search**: Vector (semantic) + BM25/FTS5 (lexical) + Graph (relationship-based) + Graph Structure (structural)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:47:- **Query Enhancement**: Fuzzy matching (Levenshtein) + acronym expansions (via hybrid-search.ts inline logic)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:61:|---> BM25 (Pure JS)            -> Keyword matches
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:82:The search pipeline (R6) decomposes retrieval into four bounded stages with strict responsibilities. Each stage has clear input/output contracts defined in `pipeline/types.ts`.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:91:Executes 5 search channels in parallel and collects raw candidates with no scoring modifications.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:96:| BM25 | `bm25-index.ts` | Pure TypeScript keyword matching |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:97:| FTS5 | `sqlite-fts.ts` | SQLite FTS5 BM25 weighted scoring |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:98:| Graph | `graph-search-fn.ts` | Causal edge traversal + typed-weighted degree (R4) |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:99:| Degree | `graph-search-fn.ts` | Structural graph discovery via typed-weighted degree |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:111:6. Intent weights — non-hybrid only (G2 double-weighting prevention: `isHybrid` boolean guard)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:149:// Vector rank: 2, BM25 rank: 5, Graph rank: 1
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:155:### BM25 (Best Matching 25)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:169:**Why BM25?**
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:175:### FTS Capability Cascade Floor
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:177:Packet `026-graph-and-context-optimization/010-fts-capability-cascade-floor` freezes the lexical capability contract that packet `002-implement-cache-warning-hooks` now consumes. `memory_search` responses expose:
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:180:- `fallbackState`: the truthful FTS capability outcome for the request.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:186:| `ok` | FTS5 compile probe passed, `memory_fts` exists, and BM25 ranking executed normally | `fts5` |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:187:| `compile_probe_miss` | `PRAGMA compile_options` does not report FTS5 support, so lexical work cannot run for this request | `unavailable` |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:188:| `missing_table` | FTS5 support is present, but `memory_fts` is missing at runtime | `unavailable` |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:189:| `no_such_module_fts5` | The SQLite engine rejects FTS5 usage with `no such module: fts5` | `unavailable` |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:190:| `bm25_runtime_failure` | The FTS5 table exists, but the `bm25(...)` ranking call fails at runtime | `unavailable` |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:248:| **TypeScript**       | `hybrid-search.ts`, `cross-encoder.ts`, `intent-classifier.ts`, `bm25-index.ts`             |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:289:| `vector-index-queries.ts`  | -      | TypeScript | Query builders and search operations for vector index |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:292:| `hybrid-search.ts`         | ~900   | TypeScript | Orchestrates vector/FTS/BM25/graph/degree fusion via adaptive RRF |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:296:| `bm25-index.ts`            | ~280   | TypeScript | Pure TypeScript BM25 (REQ-028, v1.2.0)              |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:301:| `graph-search-fn.ts`       | -      | TypeScript | Graph-structure search channel with typed-weighted degree computation |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:313:| `sqlite-fts.ts`            | -      | TypeScript | SQLite FTS5 BM25 weighted scoring, extracted from hybrid-search for independent use |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:314:| `search-flags.ts`          | -      | TypeScript | Default-on runtime feature flags for search pipeline controls |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:315:| `search-types.ts`          | -      | TypeScript | Shared type definitions and interfaces for search modules |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:318:| `memory-summaries.ts`      | -      | TypeScript | Summary storage, embedding, and search channel for memory summaries (R8) |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:327:| `retrieval-directives.ts`  | -      | TypeScript | Retrieval directive parsing and application for search configuration |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:336:| `deterministic-extractor.ts` | -    | TypeScript | Extracts deterministic signals and fields for search processing |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:340:| `llm-cache.ts`             | -      | TypeScript | Caches LLM-assisted search transforms and helper outputs |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:341:| `llm-reformulation.ts`     | -      | TypeScript | Reformulates search queries with LLM-assisted variants |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:345:| `community-search.ts`      | -      | TypeScript | Community-level search fallback — keyword-matches community summaries, returns member IDs |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:348:| `search-utils.ts`          | -      | TypeScript | Shared utility helpers used across search modules |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:349:| `session-state.ts`         | -      | TypeScript | Tracks per-session search state and retrieval context |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:361:   hybrid-search.ts -> Expand acronyms + fix typos (inline)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:368:   vector-index.ts -> Vector search (semantic)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:369:   bm25-index.ts -> BM25 search (keyword)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:370:   graph (via ../cognitive/co-activation.ts) -> Relationship search
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:371:   graph-search-fn.ts (graph structure) -> Structural graph search
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:379:   hybrid-search.ts -> Orchestrate multi-source fusion
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:415:| `ENABLE_BM25`            | `true`   | Enable BM25 lexical search (legacy compatibility gate) |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:421:| `SPECKIT_MEMORY_SUMMARIES`| `true`  | Enable memory summary generation and search channel (R8) |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:439:**BM25 Parameters** (hardcoded, tuned):
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:468:- `handlers/memory-index.ts`: keeps 3-source indexing and `includeSpecDocs` wiring aligned with search expectations.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:483:### BM25 Index Features
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:508:// 1. Vector search (semantic similarity)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:509:// 2. BM25/FTS5 search (keyword matching)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:510:// 3. Graph search (relationship traversal, 1.5x boost)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:511:// 4. Graph-structure search (structural discovery)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:518:hybridSearch("authentication", { specFolder: "specs/<###-spec-name>" })
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:522:- If BM25 disabled: Vector + FTS5 only
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:558:// Avoids redundant API calls for identical searches
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:563:// Track P95 latency (last 100 searches)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:576:**Purpose**: Generate TF-IDF extractive summaries of memory content and expose them as a search channel. Gated via `SPECKIT_MEMORY_SUMMARIES`.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:599:| **Storage** | Summaries stored with embeddings in SQLite for vector search |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:600:| **Search Channel** | `querySummaryEmbeddings()` provides cosine similarity search over stored summaries |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:643:**R4: Typed-Weighted Degree** (`graph-search-fn.ts`):
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:720:**Lexical Normalization + BM25 Document Text** (`bm25-index.ts`):
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:721:`buildBm25DocumentText()` builds the canonical lexical document from title, content, trigger phrases, and folder metadata. `normalizeLexicalQueryTokens()` is shared by BM25 and SQLite FTS flows so lexical matching stays aligned across search channels.
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:748:**Degree Cache Invalidation** (`graph-search-fn.ts`):
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:757:| **research** | Inf | Inf | 3.0x | 2.0x | 1.0x | 0.5x |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:760:`Infinity` strategy: constitutional and critical tiers with decision/research context never decay. Gated via `SPECKIT_CLASSIFICATION_DECAY` (default ON).
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:769:Selection tracking writes to a separate `learned_triggers` column (NOT FTS5 index). Safeguards include separate-column isolation, 30-day TTL, 100+ stop words denylist, rate caps (3 terms/selection, 8 terms/memory), top-3 exclusion, a cooldown period, <72h memory exclusion, rollback support, and provenance audit logging. Query weight: **0.7x** of organic triggers. Gated via `SPECKIT_LEARN_FROM_SELECTION` (default ON; set to `false` to disable).
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:782:import { init, unifiedSearch } from './hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:794:  enableGraph: true,              // Include graph search
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:808:import { unifiedSearch } from './hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:842:### BM25 Direct Access
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:850:  const results = bm25Index.getIndex().search('authentication', {
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:880:Sprint 8 delivered a comprehensive remediation pass across the search subsystem:
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:888:- FTS5 double-tokenization fix in learned feedback isolation (D2)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:893:- Dead code removal: ~360 lines across scoring, search, and graph modules
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:927:| `sqlite-vec`     | Vector search extension |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:933:| `configs/search-weights.json` | Max triggers per memory, scoring weights (loaded via SERVER_DIR) |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:944:### Research References
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:947:- **BM25**: Robertson & Walker "Okapi at TREC-3" (1994)
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:955:| REQ-011 | RRF fusion enhancement           | hybrid-search.ts                |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:958:| REQ-014 | BM25 hybrid search               | bm25-index.ts, hybrid-search.ts |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:959:| REQ-018 | Query expansion (fuzzy)          | hybrid-search.ts                |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:960:| REQ-027 | Fuzzy acronym matching           | hybrid-search.ts                |
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:961:| REQ-028 | Pure TypeScript BM25             | bm25-index.ts                   |
.opencode/skills/system-spec-kit/mcp_server/tests/structural-contract.vitest.ts:46:    isCocoIndexAvailable: vi.fn(() => false),
.opencode/skills/system-spec-kit/mcp_server/tests/structural-contract.vitest.ts:94:    expect(contract.recommendedAction).toContain('code_graph_query');
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-discovery.ts:541: * This is a lightweight pre-filter, NOT a replacement for vector search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-discovery.ts:543: * @param query  - User search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-discovery.ts:544: * @param cache  - Loaded DescriptionCache to search against.
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-discovery.ts:1100: * @param query     - User search query.
.opencode/skills/system-spec-kit/mcp_server/tests/m8-trust-state-vocabulary.vitest.ts:18://   3. code_graph_query emits a readiness block with canonical vocabulary
.opencode/skills/system-spec-kit/mcp_server/tests/m8-trust-state-vocabulary.vitest.ts:114:describe('M8 — code_graph_query readiness vocabulary (T-CGQ-11 / R22-001, R23-001)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:7:// With dependency-injected mock search functions, report formatting,
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:46: * Create a mock search function that returns different results
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:433:      const searchSpy = vi.fn<AblationSearchFn>(() => []);
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:436:      const report = await runAblation(searchSpy, {
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:445:      expect(searchSpy).not.toHaveBeenCalled();
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:455:    it('computes baseline and ablated recalls with mock search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:517:    it('handles async search function', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:533:      // Async search function
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:682:    it('returns null gracefully on search function error', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1057:    // Strategy: Use known ground truth with a mock search function where
.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1079:    // Build a search function where vector uniquely contributes some results
.opencode/skills/system-spec-kit/mcp_server/tests/session-learning.vitest.ts:6:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/session-boost.vitest.ts:4:import * as sessionBoost from '../lib/search/session-boost';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:19:  generateCacheKey: vi.fn(() => 'memory-search-ux-hooks'),
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:26:vi.mock('../lib/search/pipeline', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:30:      stage1: { searchType: 'hybrid', channelCount: 2, candidateCount: 7, constitutionalInjected: 0, durationMs: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:55:    _searchType: string,
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:85:vi.mock('../lib/search/artifact-routing', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:90:vi.mock('../lib/search/intent-classifier', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:97:vi.mock('../lib/search/session-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:101:vi.mock('../lib/search/causal-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:125:import { handleMemorySearch } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:126:import * as pipeline from '../lib/search/pipeline';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:127:import { clearCursorStore } from '../lib/search/progressive-disclosure';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:128:import { manager as retrievalSessionStateManager } from '../lib/search/session-state';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:134:describe('memory_search UX hook integration', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:147:  it('adds progressive disclosure payloads and session state to search responses', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-ux-hooks.vitest.ts:248:        stage1: { searchType: 'hybrid', channelCount: 2, candidateCount: 4, constitutionalInjected: 0, durationMs: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/degree-computation.vitest.ts:19:} from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/degree-computation.vitest.ts:220:        '[graph-search-fn] Constitutional exclusion lookup failed; returning zero scores for safety'
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:509:      vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:510:        const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:517:      vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:518:        const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:620:      // from tripping vector_search dim validation; tests that need to simulate
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:848:        vi.doMock('../lib/search/vector-index-mutations', options.vectorIndexMutationsModuleFactory as any);
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:892:      vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:893:        const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:900:      vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:901:        const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1054:      vi.doUnmock('../lib/search/vector-index-mutations');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1060:      vi.doUnmock('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1061:      vi.doUnmock('../lib/search/search-flags.js');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1877:    it('labels research root packets correctly in the Tier 3 prompt body', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1902:        specFolderSegments: ['system-spec-kit', '999-research-root'],
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1903:        specExtraFrontmatter: ['type: "research"'],
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1912:          specFolder: '999-research-root',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:1928:      expect(promptBody).toContain('PACKET_KIND: research');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:2432:    // vector_search with the harness's tiny fixture embedding. Requires a
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-save.vitest.ts:3445:          const actual = await vi.importActual<typeof import('../lib/search/vector-index-mutations')>('../lib/search/vector-index-mutations');
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:27:vi.mock('../lib/search/pipeline', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:34:    _searchType: string,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:63:vi.mock('../lib/search/artifact-routing', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:68:vi.mock('../lib/search/intent-classifier', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:75:vi.mock('../lib/search/session-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:79:vi.mock('../lib/search/causal-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:89:import { handleMemorySearch } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-constitutional-memory.vitest.ts:183:        stage1: { searchType: 'hybrid', channelCount: 2, candidateCount: 4, constitutionalInjected: 1, durationMs: 1 },
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-utils.ts:4:// Extracted from handlers/memory-search.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-utils.ts:5:// Small, stateless utility functions used during search:
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-utils.ts:18: * Minimal row shape for search utility functions.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-utils.ts:139: * Build a cache key arguments object from search parameters.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-utils.ts:234: * Apply artifact routing weights to search results.
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:25:        preferredTool: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:89:describe('memory_context advisory metadata', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:121:    vi.doMock('../handlers/memory-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:140:        nextActions: ['Use code_graph_query'],
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:152:      preferredTool: 'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:155:    expect(parsed.data.structuralRoutingNudge.message).toContain('Prefer `code_graph_query`');
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:180:    vi.doMock('../handlers/memory-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:281:        recommendedAction: 'Structural context available. Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts:296:      'Structural context available. Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:4:// Phase B T018: Community-level search as fallback channel.
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:6:// When primary search returns weak or zero results, this module
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:7:// searches community summaries by keyword matching and returns
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:14:import { isCommunitySearchFallbackEnabled, isCommunitySummariesEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:51:    console.warn(`[community-search] parseMemberIds failed (fail-open): ${message}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:71: * Extract meaningful search terms from a query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:94: * score. Used as a fallback channel when primary search returns weak results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:96: * @param query - The search query string
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:99: * @returns Community search results with member IDs for pipeline injection
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:101:export function searchCommunities(
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts:175:    console.warn(`[community-search] searchCommunities failed (fail-open): ${message}`);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:181:  it('T022: memory_search has tool-specific hints', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:182:    expect(TOOL_SPECIFIC_HINTS.memory_search).toBeDefined();
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:183:    expect(typeof TOOL_SPECIFIC_HINTS.memory_search).toBe('object');
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:221:  it('T029: memory_search EMBEDDING_FAILED has contextual hint', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:223:    const searchEmbedHint =
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:224:      TOOL_SPECIFIC_HINTS.memory_search?.[ERROR_CODES.EMBEDDING_FAILED];
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:225:    expect(searchEmbedHint).toBeDefined();
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:226:    expect(searchEmbedHint.hint).not.toBe(genericEmbedHint.hint);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:244:    const searchHint = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:246:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:247:    expect(searchHint).toBe(expectedSearchHint);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:300:    const searchEmbedHint = getRecoveryHint(
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:301:      'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:304:    expect(saveEmbedHint.hint).not.toBe(searchEmbedHint.hint);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:315:    const hasSearch = hasSpecificHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:356:    const searchHints = getAvailableHints('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:358:    expect(Object.keys(searchHints).length).toBeGreaterThanOrEqual(genericHintCount);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:362:    const searchHints = getAvailableHints('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:363:    const searchEmbedHint = searchHints[ERROR_CODES.EMBEDDING_FAILED];
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:365:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED];
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:366:    expect(searchEmbedHint).toBe(expectedToolHint);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:637:  it('T083: EMBEDDING_FAILED mentions BM25 fallback', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:639:    const hasBM25 =
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:640:      embedHint.hint.includes('BM25') ||
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:641:      embedHint.actions.some((a: string) => a.includes('BM25'));
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:642:    expect(hasBM25).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:669:  it('T087: QUERY_TOO_LONG suggests memory_match_triggers()', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:672:      a.includes('memory_match_triggers()')
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:713:    const toolSpecific = getRecoveryHint('memory_search', ERROR_CODES.EMBEDDING_FAILED);
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:718:      TOOL_SPECIFIC_HINTS.memory_search[ERROR_CODES.EMBEDDING_FAILED]
.opencode/skills/system-spec-kit/mcp_server/tests/recovery-hints.vitest.ts:725:    const allSearchHints = getAvailableHints('memory_search');
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/README.md:3:Core implementation for the structural code graph system. Provides file parsing, SQLite storage, graph queries, CocoIndex bridge, budget allocation, and compaction merging.
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/README.md:14:| `seed-resolver.ts` | Resolves CocoIndex file:line results to graph nodes |
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/README.md:18:| `compact-merger.ts` | 3-source merge (Memory + Code Graph + CocoIndex) for compaction |
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/README.md:24:- **CocoIndex** (semantic, external MCP): finds relevant code by concept
.opencode/skills/system-spec-kit/mcp_server/tests/memory-parser.vitest.ts:44:context_type: research
.opencode/skills/system-spec-kit/mcp_server/tests/memory-parser.vitest.ts:50:      expect(contextType).toBe('research');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-parser.vitest.ts:123:contextType: research
.opencode/skills/system-spec-kit/mcp_server/tests/memory-parser.vitest.ts:218:contextType: research
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:17:} from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:21: * Handles SQL patterns used by the committed graph-search-fn.ts:
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:107:      expect(SOURCE_TYPES.FTS).toBe('fts');
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:108:      expect(SOURCE_TYPES.BM25).toBe('bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:118:        { source: SOURCE_TYPES.FTS, results: [{ id: 2 }, { id: 1 }] },
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:119:        { source: SOURCE_TYPES.BM25, results: [{ id: 3 }, { id: 2 }] },
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:181:        { source: SOURCE_TYPES.FTS, results: [{ id: 2 }, { id: 4 }], weight: 0.8 },
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:182:        { source: SOURCE_TYPES.BM25, results: [{ id: 3 }, { id: 5 }], weight: 0.6 },
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:200:        { source: SOURCE_TYPES.FTS, results: [{ id: 1 }] },
.opencode/skills/system-spec-kit/mcp_server/tests/rrf-degree-channel.vitest.ts:253:      // Simulate what hybrid-search does: sort by degree score, pass to RRF
.opencode/skills/system-spec-kit/mcp_server/tests/phase2-integration.vitest.ts:5:import * as causalBoost from '../lib/search/causal-boost';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-trigger-fast-match.vitest.ts:25:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:7:import type { Stage2Input } from '../lib/search/pipeline/types.js';
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:33:vi.mock('../lib/search/learned-feedback.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:52:vi.mock('../lib/search/session-boost.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:56:vi.mock('../lib/search/causal-boost.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:60:vi.mock('../lib/search/anchor-metadata.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:64:vi.mock('../lib/search/validation-metadata.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:93:      searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:101:      searchType: 'vector',
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:242:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion.js');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:270:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion.js');
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking.vitest.ts:303:    const { executeStage2 } = await import('../lib/search/pipeline/stage2-fusion.js');
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:4:// Extracted from handlers/memory-search.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:5:// Collapses chunk-level search results into parent-level results,
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:15: * Internal search result row — enriched DB row used within the search handler.
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:16: * Mirrors the MemorySearchRow shape from memory-search.ts for chunk fields.
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:75: * Collapse chunk-level search hits into parent-level results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:84: * @param results - Raw search rows that may include chunk-level hits.
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:85: * @returns Parent-collapsed search rows plus reassembly statistics.
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts:240:    console.warn('[memory-search] Failed to reassemble chunked results, falling back to file reads:', message);
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:12:import { isEntityLinkingEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:92:  // Memory / search domain
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:97:  'retrieval': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:98:  'search': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:99:  'query': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:100:  'queries': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:101:  'lookup': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:142:  'semantic': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:143:  'semantics': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:144:  'ranking': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:145:  'relevance': 'search',
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:167: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:171: * nounPhrases('How does vector search indexing work?');
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:172: * // ['vector', 'search', 'indexing', 'work']
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:341: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts:374: * alias table to collect related search terms for query expansion.
.opencode/skills/system-spec-kit/mcp_server/tests/codex-session-start-hook.vitest.ts:28:        '- CocoIndex: available',
.opencode/skills/system-spec-kit/mcp_server/tests/codex-session-start-hook.vitest.ts:65:          '- CocoIndex: available',
.opencode/skills/system-spec-kit/mcp_server/tests/folder-scoring.vitest.ts:120:        { path: 'specs/project/research/iterations/iteration-001', expected: true },
.opencode/skills/system-spec-kit/mcp_server/tests/chunk-thinning.vitest.ts:135:    const richContent = '## Architecture Decisions\n\n- Use SQLite for local storage\n- Implement vector search with cosine similarity\n- Cache embeddings with content hash keys\n\n```typescript\nconst db = new Database("speckit.db");\ndb.exec("CREATE TABLE memories (id INTEGER PRIMARY KEY)");\n```\n\nThis design balances performance with simplicity.';
.opencode/skills/system-spec-kit/mcp_server/tests/chunk-thinning.vitest.ts:351:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:16:} from '../lib/search/query-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:24:} from '../lib/search/query-router';
.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:29:} from '../lib/search/channel-representation';
.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:32:} from '../lib/search/channel-enforcement';
.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:100:      const result = routeQuery('search for memory context retrieval');
.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:107:      const result = routeQuery('find all implementation details about the hybrid search pipeline including scoring normalization and channel representation enforcement mechanisms');
.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:379:      const route = routeQuery('find all implementation details about the hybrid search pipeline including scoring normalization and channel representation enforcement mechanisms');
.opencode/skills/system-spec-kit/mcp_server/tests/trigger-config-extended.vitest.ts:107:vi.mock('../lib/search/vector-index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/slug-utils-boundary.vitest.ts:14:} from '../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/tests/trace-propagation.vitest.ts:5:import * as hybridSearch from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/trace-propagation.vitest.ts:6:import * as bm25Index from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/trace-propagation.vitest.ts:7:import { formatSearchResults } from '../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/trace-propagation.vitest.ts:9:type InitDb = Parameters<typeof hybridSearch.init>[0];
.opencode/skills/system-spec-kit/mcp_server/tests/trace-propagation.vitest.ts:10:type VectorSearchFn = NonNullable<Parameters<typeof hybridSearch.init>[1]>;
.opencode/skills/system-spec-kit/mcp_server/tests/trace-propagation.vitest.ts:69:  const results = await hybridSearch.hybridSearchEnhanced(query, new Float32Array(384).fill(0.2), {
.opencode/skills/system-spec-kit/mcp_server/tests/trace-propagation.vitest.ts:99:    hybridSearch.init(createMockDb(), mockVectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:5:import * as searchApi from '../api/search';
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:8:  it('exposes the documented search barrel contract from api/search.ts', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:9:    expect(searchApi.initHybridSearch).toBeTypeOf('function');
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:10:    expect(searchApi.hybridSearchEnhanced).toBeTypeOf('function');
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:11:    expect(searchApi.fts5Bm25Search).toBeTypeOf('function');
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:12:    expect(searchApi.isFts5Available).toBeTypeOf('function');
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:13:    expect(searchApi.vectorIndex).toBeDefined();
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:14:    expect(searchApi.vectorIndex.initializeDb).toBeTypeOf('function');
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:15:    expect(searchApi.vectorIndex.closeDb).toBeTypeOf('function');
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:18:  it('keeps the top-level public barrel aligned with the eval and search facades', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:19:    expect(publicApi.hybridSearchEnhanced).toBe(searchApi.hybridSearchEnhanced);
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:20:    expect(publicApi.initHybridSearch).toBe(searchApi.initHybridSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:21:    expect(publicApi.fts5Bm25Search).toBe(searchApi.fts5Bm25Search);
.opencode/skills/system-spec-kit/mcp_server/tests/api-public-surfaces.vitest.ts:22:    expect(publicApi.vectorIndex).toBe(searchApi.vectorIndex);
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-update-constitutional-guard.vitest.ts:88:  vi.doMock('../lib/search/vector-index.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-update-constitutional-guard.vitest.ts:89:    const actual = await importOriginal<typeof import('../lib/search/vector-index.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-update-constitutional-guard.vitest.ts:99:  vi.doMock('../lib/search/bm25-index.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-crud-update-constitutional-guard.vitest.ts:100:    const actual = await importOriginal<typeof import('../lib/search/bm25-index.js')>();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:4:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:18:import { clearDegreeCacheForDb } from './graph-search-fn.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:21:  clear_search_cache,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:289:    // H3 FIX: Invalidate search cache after insert
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:290:    clear_search_cache();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:298:// Deferred indexing - entry searchable via BM25/FTS5 only
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:376:    logger.info(`Deferred indexing: Memory ${Number(row_id)} saved without embedding (BM25/FTS5 searchable)`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:556:    // H3 FIX: Invalidate search cache after update
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:557:    clear_search_cache();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:615:    clear_search_cache();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:621:  // BUG-021: Remove the BM25 document only after the source row is deleted.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:629:      // BEST-EFFORT BM25 CLEANUP MUST NOT MASK A SUCCESSFUL PRIMARY DELETE.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:771:      clear_search_cache();
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:780:        // BM25 cleanup is best-effort for bulk deletes as well.
.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:35:} from '../lib/search/channel-enforcement';
.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:36:import { QUALITY_FLOOR } from '../lib/search/channel-representation';
.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:175:      ['bm25',   [makeChannel('b1', 0.65, { title: 'BM25 Doc' })]],
.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:186:    expect((promoted as Record<string, unknown>)?.title).toBe('BM25 Doc');
.opencode/skills/system-spec-kit/mcp_server/lib/search/tfidf-summarizer.ts:4:// Feature catalog: Memory summary search channel
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:6:// (CocoIndex) vs hybrid (both).
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:8:// Phase 020: Integrated into memory_context handler for query-intent
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:11:export type QueryIntent = 'structural' | 'semantic' | 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:54:  'find', 'search', 'discover', 'locate', 'where',
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:78:  /(?:find|search)\s+(?:code|files|implementations)\s+(?:that|for|about|related)/i,
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:118: * (code graph) and semantic (CocoIndex) retrieval backends.
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:125:    return { intent: 'hybrid', confidence: 0.5, structuralScore: 0, semanticScore: 0, matchedKeywords: [] };
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:141:  // No signals at all → hybrid (run both)
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:143:    return { intent: 'hybrid', confidence: 0.5, structuralScore: 0, semanticScore: 0, matchedKeywords };
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:177:  // Ambiguous → hybrid with moderate confidence
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts:179:    intent: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-list-edge.vitest.ts:4:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/README.md:85:| Search and ranking | `hybrid-search.vitest.ts`, `bm25-index.vitest.ts`, `query-router.vitest.ts`, `dynamic-token-budget.vitest.ts`, `result-confidence-scoring.vitest.ts` | Retrieval, ranking, and profile/trace behavior |
.opencode/skills/system-spec-kit/mcp_server/tests/README.md:86:| Handler and protocol surface | `handler-memory-search.vitest.ts`, `handler-memory-save.vitest.ts`, `mcp-input-validation.vitest.ts`, `mcp-response-envelope.vitest.ts`, `startup-checks.vitest.ts` | MCP entrypoints and server-facing responses |
.opencode/skills/system-spec-kit/mcp_server/tests/concept-extraction.vitest.ts:8:} from '../lib/search/entity-linker';
.opencode/skills/system-spec-kit/mcp_server/tests/concept-extraction.vitest.ts:17:      expect(nounPhrases('Semantic Search')).toEqual(['semantic', 'search']);
.opencode/skills/system-spec-kit/mcp_server/tests/concept-extraction.vitest.ts:37:        ['search'],
.opencode/skills/system-spec-kit/mcp_server/tests/concept-extraction.vitest.ts:38:        ['semantic', 'search'],
.opencode/skills/system-spec-kit/mcp_server/tests/concept-extraction.vitest.ts:43:      expect(expansionTerms).not.toContain('search');
.opencode/skills/system-spec-kit/mcp_server/tests/concept-extraction.vitest.ts:47:      const expansionTerms = getConceptExpansionTerms(['search', 'embedding'], [], 2);
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-health-edge.vitest.ts:4:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/deferred-features-integration.vitest.ts:16:} from '../lib/search/entity-linker';
.opencode/skills/system-spec-kit/mcp_server/tests/deferred-features-integration.vitest.ts:25:import { generateSummary, computeTfIdf } from '../lib/search/tfidf-summarizer';
.opencode/skills/system-spec-kit/mcp_server/tests/deferred-features-integration.vitest.ts:26:import { generateAndStoreSummary, querySummaryEmbeddings, checkScaleGate } from '../lib/search/memory-summaries';
.opencode/skills/system-spec-kit/mcp_server/tests/deferred-features-integration.vitest.ts:35:} from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/deferred-features-integration.vitest.ts:345:    it('applyGraphSignals modifies search result scores', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/deferred-features-integration.vitest.ts:458:        'The search pipeline processes queries through four stages. ' +
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-impl.ts:4:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-prefix-matching.vitest.ts:7:} from '../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-prefix-matching.vitest.ts:27: * Minimal raw search result — only needs id, spec_folder, file_path.
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-prefix-matching.vitest.ts:44: * Pure-logic mirror of the prefix-matching algorithm from search-results.ts
.opencode/skills/system-spec-kit/mcp_server/tests/anchor-prefix-matching.vitest.ts:335:      'test-search',
.opencode/skills/system-spec-kit/mcp_server/tests/causal-edges-unit.vitest.ts:7:import { clearDegreeCache, computeDegreeScores } from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/causal-edges-unit.vitest.ts:694:     R-007-12: Generation counter for memory_search cache invalidation
.opencode/skills/system-spec-kit/mcp_server/tests/causal-edges-unit.vitest.ts:773:    // 008/D17: confirm the search-utils cache key threads the generation
.opencode/skills/system-spec-kit/mcp_server/tests/causal-edges-unit.vitest.ts:776:    // wiring at memory_search level. This test verifies the gating
.opencode/skills/system-spec-kit/mcp_server/tests/causal-edges-unit.vitest.ts:779:    it('R-007-12-G7: search-utils cache-args gates causalEdgesGeneration on enableCausalBoost', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/causal-edges-unit.vitest.ts:781:      const url = new URL('../lib/search/search-utils.ts', import.meta.url);
.opencode/skills/system-spec-kit/mcp_server/lib/search/dynamic-token-budget.ts:11:import { isDynamicTokenBudgetEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-context.ts:4:// LLM-oriented compact graph neighborhoods with CocoIndex seed support.
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-context.ts:5:// Provides the code_graph_context MCP tool implementation.
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-context.ts:28:  profile?: 'quick' | 'research' | 'debug';
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-context.ts:95:    case 'research':
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-context.ts:267:  actions.push('Use `mcp__cocoindex_code__search` for semantic discovery of related code');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:28:    vi.doMock('../lib/search/intent-classifier', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:49:    vi.doMock('../handlers/memory-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:113:    vi.doMock('../lib/search/session-transition', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:122:    vi.doMock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:125:    vi.doMock('../lib/search/folder-discovery', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:127:      discoverSpecFolder: vi.fn(() => 'system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement'),
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:129:    vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:145:      input: 'find the hybrid rag memory database refinement spec and related context',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:152:        specFolder: 'system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:158:          folder: 'system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:82:      const key1 = generateCacheKey('memory_search', args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:83:      const key2 = generateCacheKey('memory_search', args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:88:      const key1 = generateCacheKey('memory_search', { query: 'auth' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:89:      const key2 = generateCacheKey('memory_search', { query: 'login' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:95:      const key1 = generateCacheKey('memory_search', args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:352:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:353:      const key2 = generateCacheKey('memory_search', { query: 'test2' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:355:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:356:      set(key2, 'value2', { toolName: 'memory_search' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:358:      const invalidated = invalidateByTool('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:366:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:369:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:380:      const key1 = generateCacheKey('memory_search', { query: 'test1' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:383:      set(key1, 'value1', { toolName: 'memory_search' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:394:      const searchKey = generateCacheKey('memory_search', { query: 'test' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:395:      const triggerKey = generateCacheKey('memory_match_triggers', { prompt: 'test' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:396:      set(searchKey, 'search_result', { toolName: 'memory_search' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:397:      set(triggerKey, 'trigger_result', { toolName: 'memory_match_triggers' });
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:398:      expect(has(searchKey)).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:401:      expect(has(searchKey)).toBe(false);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:423:      const key = generateCacheKey('memory_search', args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:427:        'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:436:      expect(invalidateByTool('memory_search')).toBe(0);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:439:      const second = withCache('memory_search', args, async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:589:      const key = generateCacheKey('memory_search', args);
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:593:        'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/tool-cache.vitest.ts:603:      const second = withCache('memory_search', args, async () => 'fresh-after-shutdown');
.opencode/skills/system-spec-kit/mcp_server/tests/trigger-extractor.vitest.ts:3:// TF-IDF + N-gram hybrid trigger phrase extraction
.opencode/skills/system-spec-kit/mcp_server/tests/trigger-extractor.vitest.ts:190:      > Important: The memory architecture supports both semantic and keyword search.
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:23:    doc: '01-1-search-pipeline-features-speckit.md',
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:28:    doc: '01-1-search-pipeline-features-speckit.md',
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:33:    doc: '01-1-search-pipeline-features-speckit.md',
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:38:    doc: '01-1-search-pipeline-features-speckit.md',
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:50:    source: 'lib/search/vector-index-store.ts',
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:60:    source: 'lib/search/vector-index-store.ts',
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:65:  '01-1-search-pipeline-features-speckit.md',
.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:76:  '01-1-search-pipeline-features-speckit.md',
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:10:// P1-9  Fetch limit — search results respect the limit parameter
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:27:        '../lib/search/vector-index-schema.ts'
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:42:        '../lib/search/vector-index-schema.ts'
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:56:        '../lib/search/vector-index-schema.ts'
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:77:        '../lib/search/query-expander.ts'
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:88:      const { expandQuery } = await import('../lib/search/query-expander');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:105:      const { expandQuery } = await import('../lib/search/query-expander');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:115:    it('sanitizeFTS5Query truncates input at 2000 characters', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:116:      const { sanitizeFTS5Query } = await import('../lib/search/bm25-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:119:      const result = sanitizeFTS5Query(longInput);
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:210:     P1-9: Fetch Limit — search results respect limit parameter
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:230:    it('BM25 search respects the limit parameter', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:231:      const { BM25Index } = await import('../lib/search/bm25-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:233:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:236:        index.addDocument(`doc-${i}`, `memory search retrieval context ${i} testing`);
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:240:      const results = index.search('memory search', limit);
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:245:    it('BM25 search with limit=0 returns empty array', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:246:      const { BM25Index } = await import('../lib/search/bm25-index');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:248:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:249:      index.addDocument('doc-1', 'memory search retrieval context testing');
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:251:      const results = index.search('memory', 0);
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:255:    it('DEFAULT_LIMIT is 20 in hybrid search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:259:      const hybridPath = path.resolve(
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:261:        '../lib/search/hybrid-search.ts'
.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:263:      const source = fs.readFileSync(hybridPath, 'utf8');
.opencode/skills/system-spec-kit/mcp_server/tests/graph-roadmap-finalization.vitest.ts:6:} from '../lib/search/pipeline/ranking-contract';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-roadmap-finalization.vitest.ts:7:import { createUnifiedGraphSearchFn } from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-roadmap-finalization.vitest.ts:207:    const searchFn = createUnifiedGraphSearchFn(mockDb);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-roadmap-finalization.vitest.ts:210:      const results = searchFn('graph latency probe', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/budget-allocator.vitest.ts:34:      // CocoIndex and triggered are empty, their floors + overflow go to others
.opencode/skills/system-spec-kit/mcp_server/lib/search/confidence-scoring.ts:87:/** Request-level quality assessment (one per search call). */
.opencode/skills/system-spec-kit/mcp_server/lib/search/confidence-scoring.ts:322:export { isResultConfidenceEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-trigger-perf-benchmark.vitest.ts:47:vi.mock('../lib/search/vector-index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/community-detection.vitest.ts:150:    insertMemory(db, 1, 'Causal Search', 'specs/search', 'critical');
.opencode/skills/system-spec-kit/mcp_server/tests/community-detection.vitest.ts:151:    insertMemory(db, 2, 'Vector Ranking', 'specs/search', 'important');
.opencode/skills/system-spec-kit/mcp_server/tests/community-detection.vitest.ts:152:    insertMemory(db, 3, 'Embedding Pipeline', 'specs/search', 'important');
.opencode/skills/system-spec-kit/mcp_server/lib/search/channel-enforcement.ts:7:// Use inside the hybrid-search pipeline after RRF/RSF fusion.
.opencode/skills/system-spec-kit/mcp_server/lib/search/channel-enforcement.ts:20:/** A fused result item returned from the search pipeline. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/channel-enforcement.ts:65: * Apply channel min-representation enforcement to a set of fused search results.
.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:22:  'tool-schemas.js': 880,           // actual: 862 — Expanded MCP schema set + Sprint 019: Zod schema integration, ingest tools, Phase 024 session_bootstrap, and newer graph/search tool contracts
.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:24:  'formatters/search-results.js': 536, // actual: 536 — Search result formatting + Sprint 019/020 trace and session-transition envelope support
.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:25:  'handlers/memory-search.js': 1450, // actual: 762 — Complex search logic with multiple strategies + Pipeline V2 integration
.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:47:vi.mock('../lib/search/vector-index.js', () => mockedDbDeps);
.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:105:    'handlers/memory-search.js',
.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:112:    'formatters/search-results.js',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-session-learning.vitest.ts:7:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/unit-tier-classifier-types.vitest.ts:84:      const searchResult = {
.opencode/skills/system-spec-kit/mcp_server/tests/unit-tier-classifier-types.vitest.ts:98:      const r = tierClassifier.classifyTier(searchResult);
.opencode/skills/system-spec-kit/mcp_server/tests/unit-tier-classifier-types.vitest.ts:159:    // T-TC-11: Stats with search-enriched objects
.opencode/skills/system-spec-kit/mcp_server/tests/working-memory.vitest.ts:430:        sourceTool: 'context_search',
.opencode/skills/system-spec-kit/mcp_server/tests/working-memory.vitest.ts:440:      expect(row?.source_tool).toBe('context_search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-types.ts:5: * Function signature for graph-based lexical search helpers.
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/startup-brief.ts:10:import { isCocoIndexAvailable } from '../../lib/utils/cocoindex-path.js';
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/startup-brief.ts:141:    `- CocoIndex: ${args.cocoIndexAvailable ? 'available' : 'missing'}`,
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/startup-brief.ts:241:      lines.push('Orientation: use code graph highlights for structural entry points and call paths; use CocoIndex for semantic discovery when the symbol or file is still unknown.');
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/startup-brief.ts:304:  const cocoIndexAvailable = isCocoIndexAvailable();
.opencode/skills/system-spec-kit/mcp_server/lib/search/progressive-disclosure.ts:4:// REQ-D5-005: Progressive disclosure for search results
.opencode/skills/system-spec-kit/mcp_server/lib/search/progressive-disclosure.ts:102: * const queryHash = hashQuery('memory search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/progressive-disclosure.ts:298: * const continuation = createCursor(results, 5, 'memory search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/progressive-disclosure.ts:429: * const response = buildProgressiveResponse(results, 5, 'memory search');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:6:import { detectEvidenceGap } from '../lib/search/evidence-gap-detector';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:10:   Simulates the full hybridSearchEnhanced() flow from spec 138.
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:54:  // Simulate vector + FTS5 + graph returning mixed results
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:127:function hybridSearchEnhanced(query: string, mode: string, flags: Record<string, boolean>): EnhancedMCPResponse {
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:190:    const response = hybridSearchEnhanced('fix auth token error', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:197:    const response = hybridSearchEnhanced('explain architecture', 'deep', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:205:    const response = hybridSearchEnhanced('find spec for auth', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:214:    const response = hybridSearchEnhanced('fix bug in login', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:224:    const response = hybridSearchEnhanced('bake bread recipe', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:237:    const response = hybridSearchEnhanced('fix auth error', 'auto', ALL_FLAGS_OFF);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:246:    const withFlags = hybridSearchEnhanced('understand architecture', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:247:    const withoutFlags = hybridSearchEnhanced('understand architecture', 'auto', ALL_FLAGS_OFF);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:256:    const fixBug = hybridSearchEnhanced('fix the login bug', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:257:    const understand = hybridSearchEnhanced('explain the login system', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:265:  it('T9: deep mode search still returns valid results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:266:    const response = hybridSearchEnhanced('fix login error', 'deep', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:274:    const response = hybridSearchEnhanced('test query', 'auto', ALL_FLAGS_ON);
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:420:    const { expandQuery } = await import('../lib/search/query-expander');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:428:    const { expandQuery } = await import('../lib/search/query-expander');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:435:    const { expandQuery } = await import('../lib/search/query-expander');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:442:    const { expandQuery } = await import('../lib/search/query-expander');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:454:   Ensures hybrid retrieval and graph coverage checks keep
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:459:  it('hybridAdaptiveFuse returns standard results when SPECKIT_ADAPTIVE_FUSION is off', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:460:    const { hybridAdaptiveFuse } = await import('../../shared/algorithms/adaptive-fusion');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:466:    // When flag is off, hybridAdaptiveFuse returns standard fusion results.
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:467:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:473:    const { predictGraphCoverage } = await import('../lib/search/evidence-gap-detector');
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:145:  it('routes research findings to research doc', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:148:      text: 'Research finding: the upstream library has a race condition on concurrent reads, based on cited source analysis.',
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:152:    expect(decision.category).toBe('research_finding');
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:153:    expect(decision.target.docPath).toBe('research/research.md');
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:366:        category: 'research_finding',
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:368:        target_doc: 'research/research.md',
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:400:        research_finding: [{ id: 'rf', label: 'research', sourceShape: 'test', tags: ['research'], negativeHints: [], chunk: 'research-prototype' }],
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:419:        case 'research-prototype':
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:458:        research_finding: [{ id: 'rf', label: 'research', sourceShape: 'test', tags: ['research'], negativeHints: [], chunk: 'research-prototype' }],
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:477:        case 'research-prototype':
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:585:    expect(system).toContain('Context: This system uses a 3-level resume ladder (handover.md -> _memory.continuity in implementation-summary.md -> canonical spec docs). metadata_only saves always target implementation-summary.md. The router classifies into 8 categories: narrative_progress, narrative_delivery, decision, handover_state, research_finding, task_update, metadata_only, drop.');
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:645:  it('routes research finding text to the research doc', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:647:      id: 'np-research-1',
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:648:      text: 'Research finding: the upstream vector store library uses cosine similarity by default and does not support inner-product distance without a configuration change.',
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:652:    expect(decision.category).toBe('research_finding');
.opencode/skills/system-spec-kit/mcp_server/tests/content-router.vitest.ts:653:    expect(decision.target.docPath).toBe('research/research.md');
.opencode/skills/system-spec-kit/mcp_server/tests/structural-trust-axis.vitest.ts:13:import { computeResultConfidence } from '../lib/search/confidence-scoring.js';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-trigger-fast-path.vitest.ts:39:vi.mock('../lib/search/vector-index-store.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-trigger-fast-path.vitest.ts:43:vi.mock('../lib/search/vector-index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-trigger-fast-path.vitest.ts:106:import { handle_memory_match_triggers } from '../handlers/memory-triggers.js';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-trigger-fast-path.vitest.ts:178:      const response = await handle_memory_match_triggers({
.opencode/skills/system-spec-kit/mcp_server/tests/create-record-identity.vitest.ts:4:import * as bm25Index from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/create-record-identity.vitest.ts:5:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:2:import { classifyIntent } from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:3:import type { IntentType } from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:13:    name: 'understand semantic search terse-to-explanatory',
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:17:      'Find stuff related to semantic search',
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:18:      'Tell me about semantic search',
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:19:      'What does semantic search mean',
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:173:      'explain memory_context routing',
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:174:      'Please describe how memory_context routing works.',
.opencode/skills/system-spec-kit/mcp_server/tests/intent-paraphrase-stability.vitest.ts:175:      'What is the memory_context routing flow?',
.opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts:24:import { isCrossEncoderEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:2:// Validates the full search pipeline works with the graph channel
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:6:import type { GraphSearchFn } from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:28:// Mock the BM25 index so no filesystem reads are attempted.
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:29:vi.mock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:31:    search: vi.fn(() => []),
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:35:  sanitizeFTS5Query: vi.fn((q: string) => q),
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:128:  it('hybrid-search exports: init, hybridSearch, hybridSearchEnhanced, searchWithFallback, getGraphMetrics, resetGraphMetrics', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:129:    const mod = await import('../lib/search/hybrid-search');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:131:    expect(typeof mod.hybridSearch).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:132:    expect(typeof mod.hybridSearchEnhanced).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:133:    expect(typeof mod.searchWithFallback).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:138:  it('graph-search-fn exports: createUnifiedGraphSearchFn', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:139:    const mod = await import('../lib/search/graph-search-fn');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:144:    const mod = await import('../lib/search/graph-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:149:    const mod = await import('../lib/search/query-expander');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:154:    const mod = await import('../lib/search/evidence-gap-detector');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:160:    const mod = await import('../lib/search/fsrs');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:174:// Wire mock graph fn via init(), call hybridSearch(), verify graph
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:179:  let init: typeof import('../lib/search/hybrid-search').init;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:180:  let hybridSearch: typeof import('../lib/search/hybrid-search').hybridSearch;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:181:  let hybridSearchEnhanced: typeof import('../lib/search/hybrid-search').hybridSearchEnhanced;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:182:  let getGraphMetrics: typeof import('../lib/search/hybrid-search').getGraphMetrics;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:183:  let resetGraphMetrics: typeof import('../lib/search/hybrid-search').resetGraphMetrics;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:190:    const mod = await import('../lib/search/hybrid-search');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:192:    hybridSearch = mod.hybridSearch;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:193:    hybridSearchEnhanced = mod.hybridSearchEnhanced;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:209:  it('hybridSearch with useGraph:true calls the graphSearchFn and returns graph results', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:210:    const results = await hybridSearch('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:217:  it('hybridSearch with useGraph:false does NOT call the graphSearchFn', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:218:    await hybridSearch('test query', null, { useGraph: false });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:223:  it('hybridSearch with useGraph:false returns NO graph-sourced results', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:224:    const results = await hybridSearch('test query', null, { useGraph: false });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:230:  it('hybridSearchEnhanced runs without throwing', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:232:      hybridSearchEnhanced('test query', null, {})
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:236:  it('S4: hybridSearchEnhanced forwards specFolder to graphSearchFn', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:237:    await hybridSearchEnhanced('test query', null, { useGraph: true, specFolder: '003-root/007-child' });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:246:  it('getGraphMetrics().totalQueries increases after hybridSearchEnhanced calls', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:251:    await hybridSearchEnhanced('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:258:    // Run one enhanced search to accumulate a non-zero count.
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:259:    await hybridSearchEnhanced('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:291:    const { isGraphUnifiedEnabled } = await import('../lib/search/graph-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:297:    const { isGraphUnifiedEnabled } = await import('../lib/search/graph-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:304:// All hybridSearch results must have id, score, source fields.
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:310:  let init: typeof import('../lib/search/hybrid-search').init;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:311:  let hybridSearch: typeof import('../lib/search/hybrid-search').hybridSearch;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:315:    const mod = await import('../lib/search/hybrid-search');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:317:    hybridSearch = mod.hybridSearch;
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:322:    const results = await hybridSearch('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:332:    const results = await hybridSearch('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:343:    const results = await hybridSearch('test query', null, { useGraph: true });
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:351:  it('hybridSearch respects the limit option', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:353:    const results = await hybridSearch('test query', null, { useGraph: true, limit });
.opencode/skills/system-spec-kit/mcp_server/tests/evidence-gap-detector.vitest.ts:9:} from '../lib/search/evidence-gap-detector';
.opencode/skills/system-spec-kit/mcp_server/tests/evidence-gap-detector.vitest.ts:10:import type { TRMResult } from '../lib/search/evidence-gap-detector';
.opencode/skills/system-spec-kit/mcp_server/tests/transcript-planner-export.vitest.ts:7:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/compact-merger.ts:4:// Merges context from multiple sources (Memory, Code Graph, CocoIndex, Session)
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/compact-merger.ts:18:  cocoIndex: string;         // Semantic neighbors (from CocoIndex)
.opencode/skills/system-spec-kit/mcp_server/tests/query-expander.vitest.ts:5:import { expandQuery, DOMAIN_VOCABULARY_MAP } from '../lib/search/query-expander';
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:129:  it('research + important = 2.0 * 1.5 = 3.0', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:130:    const mult = getClassificationDecayMultiplier('research', 'important');
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:139:  it('research + normal = 2.0 stability increase (slower decay than standard)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:142:      const researchStability = applyClassificationDecay(baseStability, 'research', 'normal');
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:145:      expect(researchStability).toBeCloseTo(20.0, 6);
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:146:      expect(researchStability).toBeGreaterThan(normalStability);
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:150:      expect(calculateRetrievability(researchStability, elapsed))
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:229:      const result = applyClassificationDecay(10, 'research', 'normal');
.opencode/skills/system-spec-kit/mcp_server/tests/decay.vitest.ts:241:      expect(getClassificationDecayMultiplier('research', 'important')).toBeCloseTo(3.0, 6);
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:1:// TEST: memory_search per-channel eval logging (T056)
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:21:  generateCacheKey: vi.fn(() => 'memory-search-test-cache-key'),
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:27:vi.mock('../lib/search/pipeline', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:34:      stage1: { searchType: 'hybrid', channelCount: 2, candidateCount: 2, constitutionalInjected: 0, durationMs: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:78:vi.mock('../lib/search/artifact-routing', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:83:vi.mock('../lib/search/intent-classifier', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:90:vi.mock('../lib/search/session-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:94:vi.mock('../lib/search/causal-boost', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:104:import { handleMemorySearch, __testables } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:106:describe('T056: memory_search emits per-channel eval rows', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:138:  it('buildEvalChannelPayloads falls back to hybrid channel when attribution is missing', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:147:    expect(payload!.channel).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:52:  describe('maps session queries to hybrid intent', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:53:    it('previous work', () => { expect(classifyQueryIntent('what was I working on in the previous session').intent).toBe('hybrid'); });
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:54:    it('resume', () => { expect(classifyQueryIntent('resume my last session').intent).toBe('hybrid'); });
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:55:    it('prior decisions', () => { expect(classifyQueryIntent('what was the prior decision about auth').intent).toBe('hybrid'); });
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:72:  describe('session queries map to hybrid intent', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:73:    it('resume my previous work', () => { expect(classifyQueryIntent('resume my previous work').intent).toBe('hybrid'); });
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:74:    it('what was I doing last session', () => { expect(classifyQueryIntent('what was I doing last session').intent).toBe('hybrid'); });
.opencode/skills/system-spec-kit/mcp_server/tests/runtime-routing.vitest.ts:86:    it('Resume My Session → hybrid', () => { expect(classifyQueryIntent('Resume My Session').intent).toBe('hybrid'); });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:4:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:63:  vector_search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:65:  multi_concept_search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:71:  keyword_search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:72:  vector_search_enriched,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:73:  multi_concept_search_enriched,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:74:  multi_concept_keyword_search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:113:  cached_search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:114:  clear_search_cache,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:118:  enhanced_search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:147:  search_weights,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:154:  is_vector_search_available,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts:165:  isVectorSearchAvailable as is_vector_search_available_alias,
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:6:// PURPOSE: Generate structured recovery payloads when search returns
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:38:/** Structured recovery payload attached to search responses. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:48:  /** The original search query (may be null/empty if concepts were used). */
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:52:  /** Whether upstream search logic detected an evidence gap for this result set. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:222:import { isGraphFallbackEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:227: * When the search produces no results or low-confidence results, this function
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:252:    // Find memory IDs matching the routed concepts via title keyword search,
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:295:      // Take the first 3 words of the title as a search term
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:342: * Determine whether a search result set warrants recovery.
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts:372:export { isEmptyResultRecoveryEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/dead-code-regression.vitest.ts:6:import * as searchFlags from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/dead-code-regression.vitest.ts:9:import * as graphSearchFn from '../lib/search/graph-search-fn';
.opencode/skills/system-spec-kit/mcp_server/tests/dead-code-regression.vitest.ts:25:  ['../lib/search/search-flags', searchFlags as Record<string, unknown>],
.opencode/skills/system-spec-kit/mcp_server/tests/dead-code-regression.vitest.ts:28:  ['../lib/search/graph-search-fn', graphSearchFn as Record<string, unknown>],
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:15:} from '../lib/search/feedback-denylist';
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:48:} from '../lib/search/learned-feedback';
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:60:} from '../lib/search/auto-promotion';
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:78:/** Create a fresh test database with memory_index table + FTS5. */
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:101:  // Create the FTS5 table matching the real schema (NO learned_triggers!)
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:226:  it('R11-SCH03: CRITICAL - FTS5 isolation verified', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:232:  it('R11-SCH04: CRITICAL - verifyFts5Isolation throws if learned_triggers in FTS5', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:233:    // Create a deliberately wrong FTS5 table with learned_triggers
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:237:    // Drop the correct FTS5 and create a bad one
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:952:   10. INTEGRATION: FTS5 ISOLATION ACROSS ALL OPERATIONS
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:955:describe('FTS5 Isolation Integration (CRITICAL)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:965:    insertMemory(testDb, 1, { title: 'FTS5 Test Memory' });
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:979:  it('R11-FTS01: learned_triggers NOT in FTS5 after migration', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:983:  it('R11-FTS02: learned_triggers NOT in FTS5 after applying triggers', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:988:  it('R11-FTS03: learned_triggers NOT in FTS5 after recordSelection', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:993:  it('R11-FTS04: learned_triggers NOT in FTS5 after expiry', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/learned-feedback.vitest.ts:999:  it('R11-FTS05: learned_triggers NOT in FTS5 after rollback', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop-graph-query.vitest.ts:64:  it('queries uncovered research questions and reports live status metrics', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop-graph-query.vitest.ts:71:    const sessionId = 'research-query-live';
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop-graph-query.vitest.ts:75:      loopType: 'research',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop-graph-query.vitest.ts:96:      loopType: 'research',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop-graph-query.vitest.ts:102:      loopType: 'research',
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-v2.vitest.ts:10:} from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-v2.vitest.ts:25:} from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-v2.vitest.ts:28:import { isEmbeddingExpansionEnabled } from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-v2.vitest.ts:31:import { __testables as stage4Testables } from '../lib/search/pipeline/stage4-filter';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-v2.vitest.ts:312:        searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-v2.vitest.ts:320:    expect(output.metadata.searchType).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-v2.vitest.ts:381:    const { executePipeline } = await import('../lib/search/pipeline');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:9:// Core vector search implementation — pure functions, DB ops,
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:10:// Keyword search, content extraction, caching, and ranking.
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:12:type VectorIndexModule = typeof import('../lib/search/vector-index-impl');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:43:      mod = await import('../lib/search/vector-index-impl');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:246:      const tags = mod.extractTags('---\ntags: [memory, search, "vector"]\n---\n\nContent');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:248:      expect(tags).toContain('search');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:323:      const terms = mod.parseQuotedTerms('search for "exact phrase" in "another term" query');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:861:      vi.doMock('../lib/search/vector-index-store', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:862:        const actual = await importOriginal<typeof import('../lib/search/vector-index-store')>();
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:869:      const mutations = await import('../lib/search/vector-index-mutations');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1210:      vi.doMock('../lib/search/vector-index-store', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1211:        const actual = await importOriginal<typeof import('../lib/search/vector-index-store')>();
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1216:          is_vector_search_available: () => true,
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1220:      vectorMod = await import('../lib/search/vector-index-impl');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1245:        vi.doUnmock('../lib/search/vector-index-store');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1271:        triggerPhrases: ['vector', 'search'],
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1280:    it('indexMemory creates additional vector memories for search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1340:      const searchResults = vectorMod.vectorSearch(query, { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1341:      expect(Array.isArray(searchResults)).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1342:      expect(searchResults.length).toBeGreaterThan(0);
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1343:      if (searchResults.length > 0) {
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1344:        const firstResult = searchResults[0] as VectorSearchResult;
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1417:    it('vectorSearchEnriched — exported and falls back to keyword search without embedding', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1460:      const result = mod.learnFromSelection('vector search implementation testing', deferredId1!);
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1463:      // "vector", "search", "implementation" should be added (each >= 4 chars, not stop words)
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1465:      expect(mem?.trigger_phrases).toContain('search');
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1485:      const result = mod.learnFromSelection('alpha vector search', deferredId1!);
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1486:      // "alpha", "vector", "search" already exist — no new terms
.opencode/skills/system-spec-kit/mcp_server/tests/lazy-loading.vitest.ts:83:    expect(sourceCode).toContain("loadHandlerModule<MemorySearchModule>('memory-search')");
.opencode/skills/system-spec-kit/mcp_server/tests/lazy-loading.vitest.ts:85:    expect(sourceCode).not.toContain("import * as memorySearch from './memory-search'");
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts:16:import { isCausalBoostEnabled, isTypedTraversalEnabled as _isTypedTraversalEnabled, isGraphContextInjectionEnabled } from './search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts:86: * CTE walk (getNeighborBoosts) for search result amplification. The value
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts:89: *   - causal-boost: search result boost amplitude (range 0.8–1.5)
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts:149: * Delegates to the canonical flag check in search-flags.ts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts:519: * Apply causal graph boost to ranked search results, injecting
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts:529: * @param results - Ranked search results from prior pipeline stages
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts:707: * @param query - The search query string.
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/cli-matrix.vitest.ts:29:      return `TASK(agent=deep-research, model=opus, context=@${promptPath})`;
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/cli-matrix.vitest.ts:102:  const promptPath = 'spec-folder/research/prompts/iteration-001.md';
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/cli-matrix.vitest.ts:106:    expect(buildDispatchCommand(config, promptPath)).toContain('TASK(agent=deep-research');
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:17:} from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:28:vi.mock('../lib/search/pipeline/stage1-candidate-gen', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:32:vi.mock('../lib/search/pipeline/stage2-fusion', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:36:vi.mock('../lib/search/pipeline/stage3-rerank', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:40:vi.mock('../lib/search/pipeline/stage4-filter', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:62:import { executePipeline } from '../lib/search/pipeline/orchestrator';
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:71:    searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:95:    searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:3:import { enrichResultsWithAnchorMetadata } from '../lib/search/anchor-metadata';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:6:} from '../lib/search/validation-metadata';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:7:import { __testables as stage2Testables } from '../lib/search/pipeline/stage2-fusion';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:8:import type { PipelineRow } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:10:import { SQLiteVectorStore } from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:82:      'search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-result-adapter.ts:4:// Shared transport adapter for code_graph_query responses.
.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:29:} from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/eval-db.vitest.ts:225:      `).run('test search query', 'understand', 'easy');
.opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:49:  describe('hybrid queries', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:50:    it('returns hybrid for empty string', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:52:      expect(result.intent).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:56:    it('returns hybrid for ambiguous queries', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:58:      expect(result.intent).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:65:      expect(['structural', 'semantic', 'hybrid']).toContain(result.intent);
.opencode/skills/system-spec-kit/mcp_server/tests/query-intent-classifier.vitest.ts:84:      expect(result.intent).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:1:// TEST: SQLite FTS5 BM25 Search (C138-P2)
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:2:// Verifies weighted BM25 scoring via FTS5 bm25() function.
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:9:  FTS5_BM25_WEIGHTS,
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:12:} from '../lib/search/sqlite-fts';
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:16:describe('C138-P2 SQLite FTS5 BM25 Search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:35:    // Create FTS5 virtual table matching production column order
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:57:    // Populate FTS index
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:68:  // ---- T1: FTS5 table detection ----
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:79:  // ---- T2: BM25 weights are correct ----
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:80:  it('T2: FTS5_BM25_WEIGHTS has correct values', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:81:    expect(FTS5_BM25_WEIGHTS[0]).toBe(10.0); // title
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:82:    expect(FTS5_BM25_WEIGHTS[1]).toBe(5.0);  // trigger_phrases
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:83:    expect(FTS5_BM25_WEIGHTS[2]).toBe(2.0);  // file_path
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:84:    expect(FTS5_BM25_WEIGHTS[3]).toBe(1.0);  // content_text
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:87:  // ---- T3: Basic BM25 search returns results ----
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:120:  it('T6b: includeArchived preserves the same FTS result set after archived-branch cleanup', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:154:  it('T11: successful FTS search records lexicalPath=fts5 and fallbackState=ok', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:217:            all: () => [{ compile_options: 'ENABLE_FTS5' }],
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:249:            all: () => [{ compile_options: 'ENABLE_FTS5' }],
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:4:// Default-on runtime gates for search pipeline controls
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:15:// Feature catalog: Quality-aware 3-tier search fallback
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:19:export type SavePlannerMode = 'plan-only' | 'full-auto' | 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:31: * Session attention boost for search result re-ranking.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:39: * Causal graph traversal boost for search result amplification.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:59: * Token-pressure policy for memory_context.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:67: * Automatic session resume context injection for memory_context.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:107: * PI-A2: Quality-aware 3-tier search fallback chain.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:125: * the legacy mutation-first behavior. `hybrid` is reserved for future mixed
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:133:  if (raw === 'hybrid') {
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:134:    return 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:291: * Community summary generation and search channel.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:299: * R8: Memory summary generation (TF-IDF extractive summaries as search channel).
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:539: * REQ-D5-005: Progressive disclosure for search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:549: * Enables cross-turn dedup and goal-aware refinement of search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:637: * Phase B T016: Query concept expansion for hybrid search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:664: * Phase C T027: Result provenance — include graph evidence metadata in search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:665: * When enabled, search results include graphEvidence with contributing edges,
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:698: * Phase B T018: Community-level search as fallback channel.
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:699: * When primary search returns weak/no results, searches community summaries
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:719: * (quick, research, resume, debug) when no explicit profile is specified by the caller.
.opencode/skills/system-spec-kit/mcp_server/tests/tiered-injection-turnNumber.vitest.ts:183:      expect(typeof handlerExports.handle_memory_match_triggers).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:3:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:33:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:40:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:45:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:79:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:87:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:100:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:108:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:140:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:158:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/quality-gate-exception.vitest.ts:169:      specFolder: '022-hybrid-rag-fusion',
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:12:  generateCacheKey: vi.fn(() => 'gate-d-regression-embedding-semantic-search'),
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:19:vi.mock('../lib/search/pipeline', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:58:      stage1: { searchType: 'hybrid', channelCount: 3, candidateCount: 4, constitutionalInjected: 0, durationMs: 1 },
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:83:    _searchType: string,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:113:vi.mock('../lib/search/artifact-routing', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:118:vi.mock('../lib/search/intent-classifier', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:146:import { handleMemorySearch } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:147:import * as pipeline from '../lib/search/pipeline';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts:153:describe('Gate D regression embedding semantic search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:3:import type { PipelineRow } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:16:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:22:vi.mock('../lib/search/cross-encoder', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:26:vi.mock('../lib/search/local-reranker', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:39:import { __testables } from '../lib/search/pipeline/stage3-rerank';
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:40:import { executeStage3 } from '../lib/search/pipeline/stage3-rerank';
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:41:import { INTENT_LAMBDA_MAP } from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:220:        searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts:271:        searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:31:    type: 'search_shown',
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:112:    expect(FEEDBACK_SCHEMA_SQL).toContain('search_shown');
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:125:    expect(resolveConfidence('search_shown', 'strong')).toBe('strong');
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:134:    expect(resolveConfidence('search_shown')).toBe('weak');
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:139:      'search_shown',
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:160:    expect(EVENT_TYPE_CONFIDENCE['search_shown']).toBe('weak');
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:184:      'search_shown',
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:298:    logFeedbackEvent(db, makeEvent({ type: 'search_shown' }));
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:301:    const shown = getFeedbackEvents(db, { type: 'search_shown' });
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:303:    expect(shown[0].type).toBe('search_shown');
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:446:    logFeedbackEvent(db, makeEvent({ type: 'search_shown' }));
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:447:    logFeedbackEvent(db, makeEvent({ type: 'search_shown' }));
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-ledger.vitest.ts:449:    expect(getFeedbackEventCount(db, 'search_shown')).toBe(2);
.opencode/skills/system-spec-kit/mcp_server/tests/signal-vocab.vitest.ts:8:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/signal-vocab.vitest.ts:107:      const signals = detectSignals('search for memory context');
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:98:    const researchTemplatePath =
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:99:      '/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/sk-deep-research/assets/prompt_pack_iteration.md.tmpl';
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:103:    const researchRendered = renderPromptPack(researchTemplatePath, {
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:105:      research_topic: 'Deep loop coverage',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:111:      state_paths_config: '.opencode/skills/sk-deep-research/assets/deep_research_config.json',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:112:      state_paths_state_log: '.opencode/skills/sk-deep-research/runtime/state.jsonl',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:113:      state_paths_strategy: '.opencode/skills/sk-deep-research/assets/deep_research_strategy.md',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:114:      state_paths_registry: '.opencode/skills/sk-deep-research/runtime/registry.json',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:115:      state_paths_iteration_pattern: '.opencode/skills/sk-deep-research/runtime/iteration-002.md',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:116:      state_paths_delta_pattern: '.opencode/skills/sk-deep-research/runtime/deltas/iter-002.jsonl',
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:137:    expect(researchRendered).toContain('Research Topic: Deep loop coverage');
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop/prompt-pack.vitest.ts:138:    expect(researchRendered).toContain('State Log: .opencode/skills/sk-deep-research/runtime/state.jsonl');
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/ops-hardening.ts:73:    ? 'Use code_graph_query for structural lookups and keep transport shells thin.'
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:19:        memory_context: 3500,
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:20:        memory_search: 3500,
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget-enforcement.vitest.ts:22:        memory_match_triggers: 3500,
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:6:// Responsibility: Execute search channels and collect raw candidate results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:9:// Results are collected from the appropriate search channel based on search type.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:13://   - hybrid (deep mode): Query expansion + multi-variant hybrid search + dedup
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:14://   - hybrid (R12):       Embedding-based query expansion (SPECKIT_EMBEDDING_EXPANSION)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:16://   - hybrid: collectRawCandidates → falls back to vector on failure
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:34://     - Reads from the vector index and FTS5 / BM25 index (DB reads only)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:40:import * as hybridSearch from '../hybrid-search.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:42:import { isMultiQueryEnabled, isEmbeddingExpansionEnabled, isMemorySummariesEnabled, isQueryDecompositionEnabled, isGraphConceptRoutingEnabled, isLlmReformulationEnabled, isHyDEEnabled, isQuerySurrogatesEnabled, isTemporalContiguityEnabled, isQueryConceptExpansionEnabled } from '../search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:65:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:76:/** Minimum cosine similarity for multi-concept search. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:79:/** Number of constitutional results to fetch when none appear in hybrid/vector results. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:85:/** D2: Timeout for facet decomposition parallel searches (ms). */
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:426: * expansion and the additional search channels add latency without recall gain.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:430: * @param query - The original search query string.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:441:    // Deep mode: ensure at least 2 variants so the multi-search branch fires.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:443:    // generate a basic reformulation to trigger the parallel search path.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:528: * Selects and runs the appropriate search channel(s) based on `config.searchType`
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:550:    searchType,
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:567:  const hybridSearchOptions = {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:583:  // the query for the hybrid search channel, improving recall for alias-rich
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:584:  // queries (e.g. "semantic search" → also searches "retrieval", "query", etc.).
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:588:  /** Effective query for hybrid search — may be expanded by concept routing. */
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:591:  if (isGraphConceptRoutingEnabled() && searchType === 'hybrid') {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:644:  if (searchType === 'multi-concept' && Array.isArray(concepts) && concepts.length >= 2) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:647:      throw new Error('[stage1-candidate-gen] Maximum 5 concepts allowed for multi-concept search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:678:  else if (searchType === 'hybrid') {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:687:      throw new Error('[stage1-candidate-gen] Failed to generate embedding for hybrid search query');
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:690:    // Deep mode: expand query into variants and run hybrid for each, then dedup
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:695:      // sub-query facets and run hybrid search per facet. Results are merged
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:728:            // Run hybrid for the original query plus each facet, in parallel
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:740:                  return hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:743:                    hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:791:          // F1: Wrap parallel variant searches with latency budget.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:803:                const variantResults = await hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:806:                  hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:833:            `[stage1-candidate-gen] Deep query expansion failed, falling back to single hybrid: ${expandMsg}`
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:835:          // Fall through to single hybrid search below
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:837:          candidates = (await hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:840:            hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:844:        // ExpandQuery returned only the original; treat as standard hybrid
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:846:        candidates = (await hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:849:          hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:860:      // Hybrid search channel whose results are merged with the baseline.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:885:              hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:888:                hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:902:                  return hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:905:                    hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:938:            `[stage1-candidate-gen] R12 embedding expansion failed, using standard hybrid: ${r12Msg}`
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:943:      // Standard hybrid search — runs when R12 is off, suppressed by R15,
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:945:      // Phase B T016: Uses effectiveQuery (concept-expanded) for BM25 recall.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:949:          const hybridResults = (await hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:952:            hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:954:          candidates = hybridResults;
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:955:        } catch (hybridErr: unknown) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:956:          const hybridMsg =
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:957:            hybridErr instanceof Error ? hybridErr.message : String(hybridErr);
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:959:            `[stage1-candidate-gen] Hybrid search failed, falling back to vector: ${hybridMsg}`
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:962:          // Fallback: pure vector search
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:984:              reason: hybridMsg,
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:995:  else if (searchType === 'vector') {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1000:      throw new Error('[stage1-candidate-gen] Failed to generate embedding for vector search query');
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1023:  // -- Unknown search type -----------------------------------------------------
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1027:      `[stage1-candidate-gen] Unknown searchType: "${searchType}". Expected 'multi-concept', 'hybrid', or 'vector'.`
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1035:  // Exception: for hybrid search, tier/contextType are applied here because
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1037:  // For vector search, tier/contextType were already passed to vectorSearch,
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1051:  // Including it here caused all candidates to be filtered out when memory_context
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1078:  // In the current candidate set, fetch them separately via vector search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1115:        // via vector search bypass the earlier governance/context gate.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1143:  //   1. Retrieve top-3 seed results via fast BM25/FTS5 (no embedding call).
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1145:  //   3. Fan-out [original, abstract, ...variants] as additional hybrid search channels.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1151:  if (mode === 'deep' && isLlmReformulationEnabled() && searchType === 'hybrid') {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1172:              return hybridSearch.collectRawCandidates(
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1175:                hybridSearchOptions
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1232:  //   - Run a vector-only search with the pseudo-document embedding.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1239:  if (mode === 'deep' && isHyDEEnabled() && searchType === 'hybrid') {
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1279:  // Met (>5000 indexed), run a parallel search on summary embeddings and merge
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1445:        searchType,
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1454:  // P1 fix: activeChannels counts actual retrieval channels (vector, keyword/BM25),
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1455:  // while channelCount counts parallel query variants. In hybrid mode both vector
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1457:  const activeChannels = searchType === 'hybrid' ? 2 : 1;
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:1462:      searchType,
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:1:// TEST: memory_context per-channel eval logging (T056)
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:46:vi.mock('../handlers/memory-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:76:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:88:describe('T056: memory_context emits per-strategy channel eval rows', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/progressive-disclosure.vitest.ts:26:} from '../lib/search/progressive-disclosure';
.opencode/skills/system-spec-kit/mcp_server/tests/progressive-disclosure.vitest.ts:350:  it('keeps same-query cursors isolated across distinct searches', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:161:      'memory_context',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:162:      'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:163:      'memory_quick_search',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:164:      'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:191:      'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:193:      'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:296:      'memory_context', 'memory_search', 'memory_quick_search', 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:304:      'code_graph_scan', 'code_graph_query', 'code_graph_status', 'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:401:      '../lib/search/vector-index',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:402:      '../lib/search/vector-index.ts',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:403:      '../lib/search/vector-index.js',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:404:      '../lib/search/vector-index-store',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:405:      '../lib/search/vector-index-store.ts',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:406:      '../lib/search/vector-index-store.js',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:408:      '../lib/search/graph-flags',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:409:      '../lib/search/search-flags',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:410:      '../lib/search/graph-search-fn',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:411:      '../lib/search/session-boost',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:412:      '../lib/search/causal-boost',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:415:      '../lib/search/hybrid-search',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:416:      '../lib/search/bm25-index',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:430:      '../lib/search/learned-feedback',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:433:      '../lib/search/folder-discovery',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:447:      '../lib/search/local-reranker',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:759:      vi.doMock('../lib/search/graph-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:762:      vi.doMock('../lib/search/graph-flags.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:765:      vi.doMock('../lib/search/graph-search-fn', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:768:      vi.doMock('../lib/search/graph-search-fn.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:771:      vi.doMock('../lib/search/search-flags', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:772:        const actual = await vi.importActual('../lib/search/search-flags') as Record<string, unknown>;
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:780:      vi.doMock('../lib/search/search-flags.js', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:781:        const actual = await vi.importActual('../lib/search/search-flags') as Record<string, unknown>;
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:790:      vi.doMock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:799:      vi.doMock('../lib/search/vector-index.ts', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:808:      vi.doMock('../lib/search/vector-index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:817:      vi.doMock('../lib/search/vector-index-store', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:818:        const actual = await vi.importActual('../lib/search/vector-index-store.js') as Record<string, unknown>
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:836:      vi.doMock('../lib/search/vector-index-store.ts', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:837:        const actual = await vi.importActual('../lib/search/vector-index-store.js') as Record<string, unknown>
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:855:      vi.doMock('../lib/search/vector-index-store.js', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:856:        const actual = await vi.importActual('../lib/search/vector-index-store.js') as Record<string, unknown>
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:899:      vi.doMock('../lib/search/hybrid-search', () => ({ init: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:900:      vi.doMock('../lib/search/hybrid-search.js', () => ({ init: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:904:      vi.doMock('../lib/search/session-boost', () => ({ init: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:905:      vi.doMock('../lib/search/session-boost.js', () => ({ init: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:906:      vi.doMock('../lib/search/causal-boost', () => ({ init: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:907:      vi.doMock('../lib/search/causal-boost.js', () => ({ init: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:908:      vi.doMock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:912:      vi.doMock('../lib/search/bm25-index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:927:      vi.doMock('../lib/search/learned-feedback', () => ({ isLearnedFeedbackEnabled: vi.fn(() => false) }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:928:      vi.doMock('../lib/search/learned-feedback.js', () => ({ isLearnedFeedbackEnabled: vi.fn(() => false) }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1041:      vi.doMock('../lib/search/graph-lifecycle.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1069:      vi.doMock('../lib/search/local-reranker', () => ({ disposeLocalReranker: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1070:      vi.doMock('../lib/search/local-reranker.js', () => ({ disposeLocalReranker: vi.fn() }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1073:      vi.doMock('../lib/search/folder-discovery', () => ({ getSpecsBasePaths: vi.fn(() => options?.watchPaths ?? []) }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1074:      vi.doMock('../lib/search/folder-discovery.js', () => ({ getSpecsBasePaths: vi.fn(() => options?.watchPaths ?? []) }))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1295:        runAfterToolCallbacks('memory_search', 'call-1', structuredClone(result))
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1316:      expect(callArgs[0]).toBe('memory_search')
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1472:          if (name !== 'memory_search' && name !== 'memory_context' && name !== 'memory_quick_search' && name !== 'session_health') {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1480:        simulateCall('memory_search', { query: 'recent issues', sessionId: 'sess-sticky-1' })
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1533:      const memoryAwareTools = new Set<string>(['memory_search'])
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1560:      const response = await simulateCallToolHandler('memory_search', { query: 'hook validation' })
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1568:    it('T000g: memory_context resume mode invokes TM-05 compaction hook at runtime', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1569:      expect(sourceCode).toContain("name === 'memory_context' && args.mode === 'resume'")
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1580:      const memoryAwareTools = new Set<string>(['memory_context'])
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1593:            autoSurfacedContext = name === 'memory_context' && args.mode === 'resume'
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1614:      const response = await simulateCallToolHandler('memory_context', {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1626:    it('T000h: memory_context non-resume mode keeps SK-004 memory-aware path', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1627:      expect(sourceCode).toContain("name === 'memory_context' && args.mode === 'resume'")
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1636:      const memoryAwareTools = new Set<string>(['memory_context'])
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1649:            autoSurfacedContext = name === 'memory_context' && args.mode === 'resume'
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1668:      const response = await simulateCallToolHandler('memory_context', {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1868:        'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1869:        'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1895:          'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:1896:          'Graph retrieval: memory_search supports retrievalLevel (local/global/auto) for entity-level or community-level search. Graph provenance visible via graphEvidence in results.',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2089:      const response = errorsModule!.buildErrorResponse!('memory_search', testError, { query: 'test' })
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2107:      const hint = errorsModule!.getRecoveryHint!('memory_search', 'UNKNOWN_TOOL')
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2140:    it('T28: L1 budget = 3500 (memory_context)', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2145:      expect(layerDefs!.getTokenBudget!('memory_context')).toBe(3500)
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2148:    it('T28b: L2 budget = 3500 (memory_search)', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2153:      expect(layerDefs!.getTokenBudget!('memory_search')).toBe(3500)
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2229:    const expectedAwareTools = ['memory_context', 'memory_search', 'memory_match_triggers', 'memory_list', 'memory_save', 'memory_index_scan']
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2263:      expect(hooksModule!.extractContextHint!({ query: 'test search' })).toBe('test search')
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2323:      expect(hooksModule!.extractContextHint!({ concepts: ['memory', 'search'] })).toBe('memory search')
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2355:      expect(() => validateInputLengths({ query: 'normal search query' })).not.toThrow()
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2610:      'memory_context': '[L1:Orchestration]',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2611:      'memory_search': '[L2:Core]',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2612:      'memory_match_triggers': '[L2:Core]',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2657:    it('T000e: memory_context supports optional tokenUsage (0.0-1.0)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2658:      expect(toolSchemasCode).toMatch(/name:\s*'memory_context'[\s\S]*?tokenUsage:\s*\{\s*type:\s*'number'/)
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2773:      { module: './lib/search/vector-index.js', name: 'Vector index' },
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2777:      { module: './lib/search/hybrid-search.js', name: 'Hybrid search' },
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2778:      { module: './lib/search/bm25-index.js', name: 'BM25 index' },
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2840:        'Key tools: memory_context, memory_search, memory_save, memory_index_scan, memory_stats.',
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2866:      expect(result).toContain('memory_context')
.opencode/skills/system-spec-kit/mcp_server/tests/context-server.vitest.ts:2867:      expect(result).toContain('memory_search')
.opencode/skills/system-spec-kit/mcp_server/tests/reranker.vitest.ts:4:import * as mod from '../lib/search/reranker';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:28:  handleMemorySearch: vi.fn(async () => makeCanonicalSurfaceResponse('search')),
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:65:vi.mock('../lib/search/intent-classifier.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:81:vi.mock('../handlers/memory-search.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:93:vi.mock('../lib/search/search-flags.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:137:vi.mock('../lib/search/vector-index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:143:function makeCanonicalRows(surface: 'search' | 'triggers'): Array<Record<string, unknown>> {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:169:function makeCanonicalSurfaceResponse(surface: 'search' | 'triggers') {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:275:        handler: 'search' as const,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:288:        handler: 'search' as const,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:295:        handler: 'search' as const,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:328:      if (testCase.handler === 'search') {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:333:        const searchArgs = mocks.handleMemorySearch.mock.calls[0]?.[0] as Record<string, unknown>;
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:334:        expect(searchArgs).toMatchObject({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:341:        expect(searchArgs.autoDetectIntent).toBe(false);
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:342:        expect(searchArgs.includeArchived).toBeUndefined();
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:410:  it('search handler is called with includeArchived explicitly unset (canonical-filtering contract)', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:420:    const searchArgs = mocks.handleMemorySearch.mock.calls[0]?.[0] as Record<string, unknown>;
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:428:    expect(searchArgs.includeArchived).toBeUndefined();
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:429:    expect(searchArgs.autoDetectIntent).toBe(false);
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-intent-routing.vitest.ts:430:    expect(searchArgs.includeConstitutional).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:32:import { isCrossEncoderEnabled, isMMREnabled, isLocalRerankerEnabled } from '../search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:44:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:169:  // The result set, matching the V1 hybrid-search behavior.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:300: * @param query       - The user's search query string.
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-scoring-calibration.vitest.ts:228:    // "research" context (2.0) * "important" tier (1.5) = 3.0
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-scoring-calibration.vitest.ts:229:    const adjusted = applyClassificationDecay(baseStability, 'research', 'important');
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-scoring-calibration.vitest.ts:238:    const result = applyClassificationDecay(baseStability, 'research', 'temporary');
.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-scoring-calibration.vitest.ts:244:    const contexts = ['decision', 'research', 'implementation', 'general', 'unknown'];
.opencode/skills/system-spec-kit/mcp_server/tests/index-scope.vitest.ts:57:    expect(shouldIndexForMemory('/workspace/.opencode/specs/system-spec-kit/z_future/001-research/spec.md')).toBe(false);
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store-remediation.vitest.ts:15:} from '../lib/search/vector-index-store';
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store-remediation.vitest.ts:16:import { getMemoriesByFolder, indexMemoryDeferred } from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:4:// Feature catalog: Semantic and lexical search (memory_search)
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:5:// Weighted BM25 scoring for FTS5 full-text search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:6:// Extracted from hybrid-search.ts ftsSearch() for independent
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:9:import { BM25_FTS5_WEIGHTS, normalizeLexicalQueryTokens } from './bm25-index.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:97:      .some((value) => typeof value === 'string' && value.toUpperCase().includes('ENABLE_FTS5'));
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:147: * Execute a weighted BM25 FTS5 search against memory_fts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:149: * Uses SQLite FTS5's built-in bm25() ranking function with
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:154: * @param query - Raw search query (will be sanitized)
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:156: * @returns Array of results with BM25 scores (higher = better)
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:159: * const rows = fts5Bm25Search(db, 'memory search', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:193:  const [w0, w1, w2, w3] = BM25_FTS5_WEIGHTS;
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:208:    console.warn(`[sqlite-fts] FTS5 unavailable (${capability.fallbackState}); returning empty lexical lane results`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:249:    console.warn(`[sqlite-fts] BM25 FTS5 search failed: ${msg}`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:255: * Check if the memory_fts FTS5 virtual table exists in the database.
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:257: * Used as a feature-detect before calling fts5Bm25Search, since FTS5
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:278:  BM25_FTS5_WEIGHTS as FTS5_BM25_WEIGHTS,
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:288: * BM25 FTS result and option types exposed by the SQLite FTS module.
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:1:// TEST: BM25 INDEX
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:5:  BM25Index,
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:15:} from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:18:type HybridSearchModule = typeof import('../lib/search/hybrid-search');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:20:const ORIGINAL_ENABLE_BM25 = process.env.ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:21:process.env.ENABLE_BM25 = 'true';
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:23:let hybridSearch: HybridSearchModule | null = null;
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:26:  hybridSearch = await import('../lib/search/hybrid-search');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:28:  // Hybrid-search not available
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:31:describe('BM25 Index Tests (T031-T039)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:33:    process.env.ENABLE_BM25 = 'true';
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:40:    process.env.ENABLE_BM25 = 'true';
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:44:     T031: BM25Index class instantiation
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:47:  describe('T031: BM25Index class instantiation', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:48:    it('T031.1: new BM25Index() creates instance', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:49:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:50:      expect(index).toBeInstanceOf(BM25Index);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:54:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:59:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:64:      const custom = new BM25Index(1.5, 0.5);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:65:      expect(custom).toBeInstanceOf(BM25Index);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:69:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:76:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:210:    let index: BM25Index;
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:213:      index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:217:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:221:    it('T034.2: Document stored and searchable', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:222:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:223:      const searchResult = index.search('memory', 1);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:224:      expect(searchResult.length).toBeGreaterThan(0);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:225:      expect(searchResult[0].id).toBe('doc1');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:229:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:233:    it('T034.4: Term search returns correct doc', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:234:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:235:      const results = index.search('memory search', 5);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:241:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:246:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:251:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:252:      index.addDocument('doc2', 'another document context memory retrieval testing search hybrid vector semantic');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:260:        { id: 'bulk1', text: 'first document memory search retrieval testing vector semantic hybrid bm25' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:261:        { id: 'bulk2', text: 'second document context retrieval testing memory search semantic vector hybrid' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:262:        { id: 'bulk3', text: 'third document testing memory retrieval search vector semantic bm25 hybrid' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:274:      index.addDocument('doc1', 'memory search retrieval document indexing testing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:287:    let index: BM25Index;
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:290:      index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:292:        { id: 'doc1', text: 'memory retrieval search testing document indexing vector semantic hybrid bm25' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:293:        { id: 'doc2', text: 'memory context search document retrieval testing vector semantic hybrid bm25' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:294:        { id: 'doc3', text: 'another document different context testing retrieval search vector semantic hybrid' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:315:      const idf = index.calculateIdf('search');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:321:      const terms = ['memory', 'search', 'document', 'another', 'context'];
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:328:     T036: BM25 scoring with k1=1.2, b=0.75 parameters
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:331:  describe('T036: BM25 scoring with k1=1.2, b=0.75 parameters', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:332:    let index: BM25Index;
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:335:      index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:337:        { id: 'doc1', text: 'memory memory memory retrieval search testing document indexing vector semantic' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:338:        { id: 'doc2', text: 'memory context search document retrieval testing vector semantic hybrid bm25' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:339:        { id: 'doc3', text: 'another document different context testing retrieval search vector semantic hybrid' },
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:359:      const multiQuery = tokenize('memory search');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:365:    it('T036.5: BM25 formula produces valid scores', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:371:    it('T036.6: search() returns results sorted by score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:372:      const results = index.search('memory');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:377:    it('T036.7: search() respects limit parameter', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:378:      const results = index.search('memory search', 2);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:382:    it('T036.8: search() returns all matching documents', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:383:      const idx = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:384:      idx.addDocument('sf1', 'memory retrieval search testing document indexing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:385:      idx.addDocument('sf2', 'memory retrieval search testing document indexing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:386:      const results = idx.search('memory', 10);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:392:     T037: ENABLE_BM25 feature flag controls activation
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:395:  describe('T037: ENABLE_BM25 feature flag controls activation', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:400:    it('T037.2: BM25 is enabled by default when ENABLE_BM25 is unset', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:401:      delete process.env.ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:405:    it('T037.2b: BM25 enables when the experimental flag is set', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:406:      process.env.ENABLE_BM25 = 'true';
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:411:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:416:    it('T037.4: search() works when enabled', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:417:      const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:418:      index.addDocument('test', 'memory retrieval search testing document indexing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:419:      const results = index.search('memory');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:444:      idx.addDocument('test', 'memory retrieval search testing document indexing vector semantic hybrid bm25');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:452:     T038: BM25 integration with hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:455:  describe('T038: BM25 integration with hybrid search pipeline', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:456:    it.skipIf(!hybridSearch)('T038.1: bm25Search exported from hybrid-search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:457:      expect(typeof hybridSearch!.bm25Search).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:460:    it.skipIf(!hybridSearch)('T038.2: isBm25Available exported from hybrid-search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:461:      expect(typeof hybridSearch!.isBm25Available).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:464:    it.skipIf(!hybridSearch)('T038.3: hybridSearchEnhanced exported', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:465:      expect(typeof hybridSearch!.hybridSearchEnhanced).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:468:    it.skipIf(!hybridSearch)('T038.4: isBm25Available() true when index populated', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:471:      bm25idx.addDocument('int1', 'memory retrieval search testing document indexing vector semantic hybrid integration');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:472:      bm25idx.addDocument('int2', 'context memory search testing retrieval document vector semantic hybrid integration');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:473:      const available = hybridSearch!.isBm25Available();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:481:    it.skipIf(!hybridSearch)('T038.5: bm25Search returns results via hybrid-search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:484:      bm25idx.addDocument('int1', 'memory retrieval search testing document indexing vector semantic hybrid integration');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:485:      bm25idx.addDocument('int2', 'context memory search testing retrieval document vector semantic hybrid integration');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:486:      const results = hybridSearch!.bm25Search('memory search', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:491:    it.skipIf(!hybridSearch)('T038.6: Legacy camelCase aliases available', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:492:      expect(typeof hybridSearch!.bm25Search).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:493:      expect(typeof hybridSearch!.isBm25Available).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:498:     T039: combined_lexical_search() merges FTS5 + BM25 results
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:501:  describe('T039: combined_lexical_search() merges FTS5 + BM25', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:502:    it.skipIf(!hybridSearch)('T039.1: combinedLexicalSearch exported', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:503:      expect(typeof hybridSearch!.combinedLexicalSearch).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:506:    it.skipIf(!hybridSearch)('T039.2: combinedLexicalSearch returns array', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:508:      const results = hybridSearch!.combinedLexicalSearch('test query', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:512:    it.skipIf(!hybridSearch)('T039.3: combinedLexicalSearch returns BM25 results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:515:      bm25comb.addDocument('comb1', 'memory retrieval search testing document indexing vector semantic hybrid combined');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:516:      bm25comb.addDocument('comb2', 'context memory search testing retrieval document vector semantic hybrid combined');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:517:      const results = hybridSearch!.combinedLexicalSearch('memory search', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:521:    it.skipIf(!hybridSearch)('T039.4: Results include score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:524:      bm25.addDocument('comb1', 'memory retrieval search testing document indexing vector semantic hybrid combined');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:525:      const results = hybridSearch!.combinedLexicalSearch('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:530:    it.skipIf(!hybridSearch)('T039.5: Results include source or bm25 score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:533:      bm25.addDocument('comb1', 'memory retrieval search testing document indexing vector semantic hybrid combined');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:534:      const results = hybridSearch!.combinedLexicalSearch('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:541:    it.skipIf(!hybridSearch)('T039.6: Results include combined or bm25 score', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:544:      bm25.addDocument('comb1', 'memory retrieval search testing document indexing vector semantic hybrid combined');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:545:      const results = hybridSearch!.combinedLexicalSearch('memory', { limit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:552:    it.skipIf(!hybridSearch || !isBm25Enabled())('T039.7: Respects limit parameter', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:555:      bm25.addDocument('comb1', 'memory retrieval search testing document indexing vector semantic hybrid combined');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:556:      bm25.addDocument('comb2', 'context memory search testing retrieval document vector semantic hybrid combined');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:557:      const results = hybridSearch!.combinedLexicalSearch('memory', { limit: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:561:    it.skipIf(!hybridSearch || !isBm25Enabled())('T039.8: combinedLexicalSearch returns results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:564:      bm25.addDocument('filt1', 'memory retrieval search testing document indexing vector semantic hybrid filter');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:565:      bm25.addDocument('filt2', 'memory retrieval search testing document indexing vector semantic hybrid filter');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:566:      const results = hybridSearch!.combinedLexicalSearch('memory', { limit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:571:    it.skipIf(!hybridSearch)('T039.9: Legacy alias combinedLexicalSearch available', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:572:      expect(typeof hybridSearch!.combinedLexicalSearch).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:577:describe('C138: Weighted BM25 FTS5 Enhancements', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:578:  it('C138-T1: BM25 index exports getIndex function', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:582:  it('C138-T2: DEFAULT_K1 is standard BM25 constant', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:587:  it('C138-T3: DEFAULT_B is standard BM25 constant', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:615:      trigger_phrases: ['hybrid-search', 'bm25-sync'],
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:621:    expect(text).toContain('hybrid-search');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:639:      [1, { id: 1, title: 'Auth doc', content_text: 'authentication search memory body', trigger_phrases: 'auth', file_path: 'specs/auth/1.md' }],
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:663:    const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:675:    const index = new BM25Index();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:715:    vi.doMock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:729:    vi.doMock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:778:  it('BM25 re-index fires when triggerPhrases change', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:784:  it('BM25 re-index fires when title changes', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:798:  it('BM25 re-index does NOT fire when non-trigger fields change', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:811:  it('BM25 data failures are surfaced from inside the transaction callback', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:819:      .toThrow('BM25 re-index failed: bad bm25 payload');
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:826:  if (ORIGINAL_ENABLE_BM25 === undefined) {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:827:    delete process.env.ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:829:    process.env.ENABLE_BM25 = ORIGINAL_ENABLE_BM25;
.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:5:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:4:// Resolves CocoIndex search results (file:line) to code graph nodes.
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:10:/** A seed from CocoIndex or other providers */
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:19:/** Native CocoIndex search result as a seed */
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:20:export interface CocoIndexSeed {
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:47:export type AnySeed = CodeGraphSeed | CocoIndexSeed | ManualSeed | GraphSeed;
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:75:function isCocoIndexSeed(seed: unknown): seed is CocoIndexSeed {
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:95:/** Resolve a CocoIndex seed by converting to CodeGraphSeed and delegating */
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:96:export function resolveCocoIndexSeed(seed: CocoIndexSeed): ArtifactRef {
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/seed-resolver.ts:334:  if (isCocoIndexSeed(seed)) return resolveCocoIndexSeed(seed);
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:10:import { handleMemorySearch } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:15:// The handlers (memory-context, memory-search, memory-triggers) all import
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:38:// Mock the sub-handlers (memory-search, memory-triggers) to avoid
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:41:vi.mock('../handlers/memory-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:232:          input: 'why did search ranking regress after the fusion change?',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:241:      // detected intent is forwarded to the search handler.
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:249:    it('forwards response profile through routed search strategies', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:265:    it('forwards governed scope fields through deep-mode search routing', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:286:    it('forwards governed scope fields through resume-mode search routing', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:593:    it('preserves traced resume metadata without routing resume mode through memory_search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:596:      const searchCallCountBefore = mockedHandleMemorySearch.mock.calls.length;
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:617:      expect(mockedHandleMemorySearch.mock.calls.length).toBe(searchCallCountBefore);
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:629:      const searchCallCountBefore = mockedHandleMemorySearch.mock.calls.length;
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:642:      expect(mockedHandleMemorySearch.mock.calls.length).toBe(searchCallCountBefore);
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:806:              error: 'upstream search failed',
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:810:            hints: ['retry search'],
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:833:      expect(parsed.data.error).toBe('upstream search failed');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:835:      expect(parsed.hints).toContain('retry search');
.opencode/skills/system-spec-kit/mcp_server/tests/learned-combiner.vitest.ts:26:import { isLearnedStage2CombinerEnabled } from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:150:  it('T002-A: logs a "search" event', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:152:      event_type: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:153:      query_text: 'test search query',
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:162:    const row = db.prepare(`SELECT * FROM consumption_log WHERE event_type = 'search'`).get() as Record<string, unknown>;
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:164:    expect(row.event_type).toBe('search');
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:165:    expect(row.query_text).toBe('test search query');
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:212:      event_type: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:221:    const row = db.prepare(`SELECT * FROM consumption_log WHERE event_type = 'search'`).get() as Record<string, unknown>;
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:230:      event_type: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:245:      forceLogConsumptionEvent(db, { event_type: 'search', query_text: `query ${i}`, result_count: i });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:278:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:286:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:287:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:290:    expect(stats.by_event_type['search']).toBe(2);
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:296:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 4 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:297:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 6 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:303:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 1, latency_ms: 100 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:304:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 1, latency_ms: 200 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:310:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 0, query_text: 'empty' });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:311:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 0, query_text: 'also empty' });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:312:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 5, query_text: 'got results' });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:318:    forceLogConsumptionEvent(db, { event_type: 'search', session_id: 'ses-A', result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:319:    forceLogConsumptionEvent(db, { event_type: 'search', session_id: 'ses-A', result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:320:    forceLogConsumptionEvent(db, { event_type: 'search', session_id: 'ses-B', result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:326:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:328:    const stats = getConsumptionStats(db, { event_type: 'search' });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:363:      forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'repeated query', result_count: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:366:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'unique query', result_count: 2 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:376:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'nothing found', result_count: 0 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:377:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'also nothing', result_count: 0 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:378:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'has results', result_count: 4 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:387:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'sparse query', result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:388:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'sparse query 2', result_count: 2 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:389:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'good query', result_count: 8 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:398:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'mixed sparse', result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:399:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'mixed sparse', result_count: 2 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:409:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'fix the bug', intent: 'fix_bug', result_count: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:410:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'fix the bug', intent: 'refactor', result_count: 2 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:411:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'stable query', intent: 'understand', result_count: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:412:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'stable query', intent: 'understand', result_count: 4 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:423:      forceLogConsumptionEvent(db, { event_type: 'search', session_id: 'heavy-session-001', query_text: `q${i}`, result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:425:    forceLogConsumptionEvent(db, { event_type: 'search', session_id: 'light-session', query_text: 'only one', result_count: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:436:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'unique A', result_count: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:437:    forceLogConsumptionEvent(db, { event_type: 'search', query_text: 'unique B', result_count: 7 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:458:      logConsumptionEvent(db, { event_type: 'search', query_text: 'test', result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:469:        event_type: 'search',
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:535:      logConsumptionEvent(db, { event_type: 'search', query_text: 'should not log', result_count: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:580:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 1, latency_ms: 123.456 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:587:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:593:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 1, latency_ms: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:594:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 1, latency_ms: 20 });
.opencode/skills/system-spec-kit/mcp_server/tests/consumption-logger.vitest.ts:595:    forceLogConsumptionEvent(db, { event_type: 'search', result_count: 1, latency_ms: 30 });
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/types.ts:11: * Memory search row — the canonical internal result type flowing through the pipeline.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/types.ts:124:  searchType: 'hybrid' | 'vector' | 'multi-concept';
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/types.ts:193: * Executes search channels (FTS5, semantic, trigger, graph, co-activation)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/types.ts:206:    searchType: string;
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/types.ts:208:    /** Actual retrieval channels active (vector=1, hybrid=2). Unlike channelCount which tracks query variants. */
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery-integration.vitest.ts:25:} from '../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery-integration.vitest.ts:26:import type { DescriptionCache, PerFolderDescription } from '../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery-integration.vitest.ts:27:import { isFolderDiscoveryEnabled } from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/folder-discovery-integration.vitest.ts:922:    const modulePath = path.join(__dirname, '../dist/lib/search/folder-discovery.js');
.opencode/skills/system-spec-kit/mcp_server/tests/unit-normalization-roundtrip.vitest.ts:194:        custom_search_score: 0.95,
.opencode/skills/system-spec-kit/mcp_server/tests/memory-parser-extended.vitest.ts:187:      const canonicals: ContextType[] = ['implementation', 'research', 'planning', 'general'];
.opencode/skills/system-spec-kit/mcp_server/tests/memory-parser-extended.vitest.ts:193:      const aliases = { debug: 'implementation', analysis: 'research', decision: 'planning', discovery: 'general', bug: 'implementation' };
.opencode/skills/system-spec-kit/mcp_server/tests/memory-parser-extended.vitest.ts:199:      const validTypes = new Set<ContextType>(['implementation', 'research', 'planning', 'general']);
.opencode/skills/system-spec-kit/mcp_server/tests/graph-calibration.vitest.ts:24:} from '../lib/search/graph-calibration';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-calibration.vitest.ts:31:} from '../lib/search/graph-calibration';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-calibration.vitest.ts:239:  /** Mock search: drops results when a feature is disabled. */
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-schema-compatibility.vitest.ts:3:import { SCHEMA_VERSION, validateBackwardCompatibility } from '../lib/search/vector-index-schema';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-index-scope.vitest.ts:194:  vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-index-scope.vitest.ts:195:    const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:35:This folder contains the structural code graph subsystem. It walks a workspace, parses source files via tree-sitter or the shipped regex fallback, and persists nodes (functions, classes, modules) and edges (calls, imports, contains, type_of) into a SQLite database. The graph backs the `code_graph_scan`, `code_graph_query`, `code_graph_status`, and `code_graph_context` MCP tools, and feeds the structural-context payload consumed by both MCP `session_bootstrap` and the OpenCode `compact-code-graph` plugin.
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:60:| **Blocked read contract** | `code_graph_context` returns a structured `status:"blocked"` payload when a broader full scan is required before graph answers can be trusted |
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:95:│   ├── query.ts                    # code_graph_query
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:97:│   ├── context.ts                  # code_graph_context
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:98:│   ├── ccc-status.ts               # CocoIndex status bridge
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:99:│   ├── ccc-reindex.ts              # CocoIndex reindex bridge
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:100:│   ├── ccc-feedback.ts             # CocoIndex feedback bridge
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:125:| `handlers/context.ts` | `code_graph_context` MCP handler — context-window-bounded retrieval |
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:126:| `handlers/query.ts` | `code_graph_query` MCP handler — graph traversal queries |
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:137:The subsystem exposes four operator-visible contract families: `code_graph_status`, `code_graph_context`, `code_graph_query`, and startup/compaction payloads. They share the readiness vocabulary (`readiness`, `canonicalReadiness`, `trustState`) and surface graph-quality and structured transport metadata. Both `code_graph_context` and `code_graph_query` enforce the same explicit blocked/degraded contract when readiness requires a suppressed `full_scan`, and `code_graph_query` additionally carries CALLS ambiguity resolution metadata.
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:144:| **`code_graph_context` (success path)** | `status: "ok"` | `readiness`, `canonicalReadiness`, `trustState`, `lastPersistedAt`, `anchors`, `graphContext`, `textBrief`, `metadata`, `graphMetadata` | Context reads always echo readiness so callers can judge freshness and detector provenance alongside the returned neighborhood |
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:145:| **`code_graph_context` (blocked path)** | `status: "blocked"` | `blocked`, `degraded`, `graphAnswersOmitted`, `requiredAction`, `blockReason`, `readiness`, `canonicalReadiness`, `trustState`, `lastPersistedAt` | Returned when readiness requires a full scan and inline full scans are disallowed; callers should run `code_graph_scan` before retrying |
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:146:| **`code_graph_query` (success path)** | `status: "ok"` | `readiness`, `canonicalReadiness`, `trustState`, operation results, ambiguity / selected-candidate metadata | CALLS queries on ambiguous `handle*` subjects prefer callable implementation nodes over wrapper-shadow candidates; metadata records the chosen candidate and other candidates considered |
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:147:| **`code_graph_query` (blocked path)** | `status: "blocked"` | Same shape as the `code_graph_context` blocked payload (`blocked`, `degraded`, `graphAnswersOmitted`, `requiredAction`, `blockReason`, readiness + trust) | Query reads mirror the context read contract instead of silently returning empty results when readiness requires a suppressed `full_scan` |
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:151:`code_graph_context` success payloads carry structured metadata instead of a text-only readiness hint.
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md:159:| `anchors[*]` | `source`, `provider`, `score`, `snippet`, `range` | Preserves seed provenance so CocoIndex/manual/graph-sourced anchors stay traceable |
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-denylist.vitest.ts:9:} from '../lib/search/feedback-denylist';
.opencode/skills/system-spec-kit/mcp_server/tests/feedback-denylist.vitest.ts:39:  const domainStopWords = ['memory', 'session', 'context', 'query', 'search', 'result'];
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:8:// - Simulate "search results" as fixed sets based on channel set
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:17:} from '../lib/search/query-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:24:} from '../lib/search/query-router';
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:33:  'search memory',
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:46:  'search tools',
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:61:  'optimize the search query performance',
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:80:  'investigate why the search results are returning duplicate entries when using the advanced filter with pagination',
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:94:  'implement full-text search with relevance ranking stemming stop-word filtering and approximate nearest-neighbor retrieval',
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:110: * In a real system this would invoke the actual search pipeline.
.opencode/skills/system-spec-kit/mcp_server/code_graph/tools/code-graph-tools.ts:23:  'code_graph_query',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tools/code-graph-tools.ts:25:  'code_graph_context',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tools/code-graph-tools.ts:65:    case 'code_graph_query': {
.opencode/skills/system-spec-kit/mcp_server/code_graph/tools/code-graph-tools.ts:75:    case 'code_graph_context':
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:112:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'shared', title: 'S' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:122:      { source: SOURCE_TYPES.BM25,    results: [{ id: 'shared', title: 'S' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:163:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'x', title: 'X' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:176:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'y', title: 'Y' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:186:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'z', title: 'Z' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:196:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'only-bm25', title: 'B' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:210:      { source: SOURCE_TYPES.BM25,    results: [{ id: 'partial', title: 'P' }, { id: 'all', title: 'A' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:224:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'neg-test', title: 'N' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:238:      { source: SOURCE_TYPES.BM25, results: [
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:252:      { source: SOURCE_TYPES.BM25,    results: [{ id: 'mega', title: 'M' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:254:      { source: SOURCE_TYPES.FTS,     results: [{ id: 'mega', title: 'M' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:275:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'bc', title: 'BC' }] },
.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:289:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'beta-ignored', title: 'BI' }] },
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:5:  - "search pipeline"
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:18:A four-stage retrieval pipeline that takes a search query through candidate generation, score fusion, reranking and final filtering to produce ranked memory results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34:The `pipeline/` directory implements the core retrieval pipeline behind `memory_search`. Each search request flows through four sequential stages, each with a defined I/O contract and clear responsibility boundary. The pipeline supports hybrid, vector and multi-concept search types with optional deep-mode query expansion, cross-encoder reranking, MMR diversity pruning and MPAB chunk-to-parent reassembly.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:48:| `stage1-candidate-gen.ts` | Stage 1: Candidate Generation. Runs search channels (hybrid, vector, multi-concept), applies deep-mode query expansion (R6), embedding-based expansion (R12), summary embeddings (R8), constitutional memory injection, quality threshold filtering and tier/contextType filtering. |
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:49:| `stage2-fusion.ts` | Stage 2: Fusion + Signal Integration. The single authoritative scoring point. Applies 9 signal steps in fixed order: session boost, causal boost, co-activation spreading, community co-retrieval, graph signals, FSRS testing effect, intent weights (non-hybrid only, G2 prevention), artifact routing, feedback signals, artifact limiting, anchor metadata and validation metadata scoring. |
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:63:      |  search channels, constitutional injection, quality filter
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:79:- Runs one or more search channels based on `searchType` and `mode`.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:80:- Channels: hybrid (with optional deep-mode expansion), vector, multi-concept.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:88:- G2 prevention: intent weights are applied only for non-hybrid search types.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:108:2. **G2 Double-Weighting Guard.** Intent weights are applied only for non-hybrid search types. Hybrid search incorporates intent weighting during RRF/RSF fusion internally.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:116:- `mcp_server/lib/search/` - Parent search directory containing hybrid search, vector index, cross-encoder and other search modules consumed by the pipeline.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:117:- `mcp_server/lib/ops/` - Background operations (file watcher, job queue) that feed data into the search index.
.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints-edge.vitest.ts:4:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints-edge.vitest.ts:207:    expect(hints.some((hint) => /search indexes rebuilt/i.test(hint))).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:16:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:38:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:127:  it('returns null for memory_context (prevents recursive surfacing)', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:128:    const result = await autoSurfaceAtToolDispatch('memory_context', { input: 'some context' });
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:132:  it('returns null for memory_search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:133:    const result = await autoSurfaceAtToolDispatch('memory_search', { query: 'some query' });
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:137:  it('returns null for memory_match_triggers', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:138:    const result = await autoSurfaceAtToolDispatch('memory_match_triggers', { prompt: 'some prompt' });
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:251:    await autoSurfaceAtToolDispatch('some_tool', { query: 'my search query' });
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:252:    expect(matchSpy).toHaveBeenCalledWith('my search query', 5);
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:283:    await autoSurfaceAtToolDispatch('some_tool', { concepts: ['memory', 'search'] });
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:284:    expect(matchSpy).toHaveBeenCalledWith('memory search', 5);
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:510:    const result = await autoSurfaceAtCompaction('Session context about memory search and spec kit');
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:522:    const result = await autoSurfaceAtCompaction('Session context about memory search');
.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:533:    const result = await autoSurfaceAtCompaction('Session context about memory search');
.opencode/skills/system-spec-kit/mcp_server/tests/db-dimension-integrity.vitest.ts:7:import { close_db, getEmbeddingDim, initializeDb } from '../lib/search/vector-index-store';
.opencode/skills/system-spec-kit/mcp_server/tests/session-state.vitest.ts:20:} from '../lib/search/session-state';
.opencode/skills/system-spec-kit/mcp_server/tests/retrieval-telemetry.vitest.ts:212:    recordFallback(t, 'hybrid search failed');
.opencode/skills/system-spec-kit/mcp_server/tests/retrieval-telemetry.vitest.ts:214:    expect(t.fallback.fallbackReason).toBe('hybrid search failed');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-quality-filter.vitest.ts:3:import { __testables } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-quality-filter.vitest.ts:104:describe('C138: memory-search cache args include behavior-changing parameters', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-quality-filter.vitest.ts:171:    expect(resolveRowContextType({ id: 1, contextType: 'decision', context_type: 'research' } as any)).toBe('decision');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-quality-filter.vitest.ts:174:  it('falls back to snake_case context_type for hybrid rows', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-quality-filter.vitest.ts:175:    expect(resolveRowContextType({ id: 2, context_type: 'research' } as any)).toBe('research');
.opencode/skills/system-spec-kit/mcp_server/tests/fsrs-hybrid-decay.vitest.ts:13:describe('FSRS hybrid decay policy', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/fsrs-hybrid-decay.vitest.ts:40:  it('makes applyClassificationDecay honor the hybrid no-decay override when enabled', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/fsrs-hybrid-decay.vitest.ts:48:  it('gates hybrid behavior behind SPECKIT_HYBRID_DECAY_POLICY', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:20:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:58:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:60:        data: { searchType: 'hybrid', count: 5, results: ['a', 'b', 'c', 'd', 'e'] },
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:65:      expect(envelope.data.searchType).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:97:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:108:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:135:        tool: 'memory_search'
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:143:        tool: 'memory_search'
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:152:        tool: 'memory_search'
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:157:      expect(envelope.hints).toContain('Try broadening your search query');
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:186:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:206:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:254:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:312:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:352:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:363:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:373:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:384:        tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/envelope.vitest.ts:409:        tool: 'memory_search'
.opencode/skills/system-spec-kit/mcp_server/tests/description/repair-specimens.vitest.ts:8:import type { PerFolderDescription } from '../../lib/search/folder-discovery';
.opencode/skills/system-spec-kit/mcp_server/tests/description/repair-specimens.vitest.ts:10:type DiscoveryModule = typeof import('../../lib/search/folder-discovery');
.opencode/skills/system-spec-kit/mcp_server/tests/description/repair-specimens.vitest.ts:67:  const discovery = await import('../../lib/search/folder-discovery');
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/orchestrator.ts:54: * @param config Pipeline configuration derived from search args
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-fallback.vitest.ts:28: * In production this wraps the Promise.all scatter block in hybrid-search.ts.
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-memory-tiers.vitest.ts:76:    const searchableRows = sameTopicRows.filter((row) => !isExcludedFromSearch(row.importance_tier));
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-memory-tiers.vitest.ts:77:    const ranked = applyCompositeScoring(searchableRows, {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-memory-tiers.vitest.ts:82:    expect(searchableRows).toHaveLength(3);
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-memory-tiers.vitest.ts:83:    expect(searchableRows.every((row) => row.document_type !== 'memory')).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-memory-tiers.vitest.ts:84:    expect(searchableRows.every((row) => !row.file_path.includes('/memory/'))).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:12:    vi.doUnmock('../lib/search/search-flags');
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:13:    vi.doUnmock('../lib/search/search-flags.js');
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:19:    vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:20:      const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:26:    vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:27:      const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:89:      'Post-insert enrichment was deferred; runEnrichmentBackfill when immediate graph/search freshness matters',
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:322:    vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:323:      const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:333:    vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:334:      const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:355:    vi.doMock('../lib/search/entity-linker', () => ({ runEntityLinkingForMemory: runLinkerMock }));
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:356:    vi.doMock('../lib/search/entity-linker.js', () => ({ runEntityLinkingForMemory: runLinkerMock }));
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:357:    vi.doMock('../lib/search/graph-lifecycle', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:361:    vi.doMock('../lib/search/graph-lifecycle.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:393:    vi.doMock('../lib/search/search-flags', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:394:      const actual = await importOriginal<typeof import('../lib/search/search-flags')>();
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:404:    vi.doMock('../lib/search/search-flags.js', async (importOriginal) => {
.opencode/skills/system-spec-kit/mcp_server/tests/post-insert-deferred.vitest.ts:405:      const actual = await importOriginal<typeof import('../lib/search/search-flags.js')>();
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:44:import * as memorySearchHandler from '../handlers/memory-search.js';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:46:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:47:import * as hybridSearch from '../lib/search/hybrid-search.js';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:52:const MEMORY_SEARCH_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'handlers', 'memory-search.ts'), 'utf-8');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:53:const VECTOR_INDEX_QUERIES_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'lib', 'search', 'vector-index-queries.ts'), 'utf-8');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:54:const HYBRID_SEARCH_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'lib', 'search', 'hybrid-search.ts'), 'utf-8');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:55:const VECTOR_INDEX_SCHEMA_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'lib', 'search', 'vector-index-schema.ts'), 'utf-8');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:56:const STAGE1_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'lib', 'search', 'pipeline', 'stage1-candidate-gen.ts'), 'utf-8');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:57:const STAGE2_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'lib', 'search', 'pipeline', 'stage2-fusion.ts'), 'utf-8');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:187:      expect(VECTOR_INDEX_QUERIES_SOURCE).toContain('Multi-concept search requires 2-5 concepts');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:200:    it('T626: Multi-concept requests are labeled as multi_concept search type', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:203:      // fixture and checks the response metadata contains searchType = 'multi-concept'.
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:204:      expect(MEMORY_SEARCH_SOURCE).toContain("searchType: (hasValidConcepts && concepts!.length >= 2)");
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:234:    it('T631: hybrid-search.js loads', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:235:      expect(hybridSearch).toBeTruthy();
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:238:    it('T632: hybridSearch function exported', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:239:      expect(typeof hybridSearch.hybridSearch).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:242:    it('T633: searchWithFallback function exported', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:243:      expect(typeof hybridSearch.searchWithFallback).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:246:    it('T634: FTS availability check function exists', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:247:      expect(typeof hybridSearch.isFtsAvailable).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:250:    it('T635: Hybrid search uses fusion-based ranking', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:252:      // that verifies hybridSearch output uses fuseResultsMulti ranking.
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:256:    it('T636: Hybrid combines vector + FTS', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:259:      expect(HYBRID_SEARCH_SOURCE).toContain('hybridSearchEnhanced');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:262:    it('T637: RRF fusion available for hybrid ranking', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:277:    it('T639: searchWithFallback falls back to FTS after empty hybrid results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:284:    it('T640: searchWithFallback falls back to BM25 after empty FTS results', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:388:    it.todo('multi-concept search returns ranked results from DB (requires DB fixture)');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:389:    it.todo('hybrid search fallback chain works end-to-end (requires DB fixture)');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:392:    it.todo('searchWithFallback cascades through vector -> FTS -> BM25 (requires DB fixture)');
.opencode/skills/system-spec-kit/mcp_server/tests/unit-folder-scoring-types.vitest.ts:85:        _searchScore: 0.95,
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:10:import * as intentClassifier from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:14:  hybridAdaptiveFuse,
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:151:    const result = hybridAdaptiveFuse(semantic, keyword, intent);
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:232:    const bugResult = hybridAdaptiveFuse(semantic, keyword, 'fix_bug');
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:233:    const understandResult = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:269:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:287:    const result = hybridAdaptiveFuse(semantic, keyword, 'fix_bug');
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:300:    const result1 = hybridAdaptiveFuse(semantic, keyword, 'fix_bug');
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:301:    const result2 = hybridAdaptiveFuse(semantic, keyword, 'fix_bug');
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:349:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:389:    const result = hybridAdaptiveFuse(semantic, keyword, 'understand');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-pipeline-enforcement.vitest.ts:7:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget.vitest.ts:15:} from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget.vitest.ts:21:} from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget.vitest.ts:275:   The formula lives inline in hybrid-search.ts (line ~971).
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget.vitest.ts:281:   * Replicates the inline formula from hybrid-search.ts:
.opencode/skills/system-spec-kit/mcp_server/tests/token-budget.vitest.ts:321:    // Simulate what hybrid-search.ts does: compute adjusted budget, pass to truncateToBudget
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:4:import * as searchHandler from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:5:import * as hybridSearch from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:6:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:7:import * as bm25Index from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:9:import { isMMREnabled, isTRMEnabled, isMultiQueryEnabled } from '../lib/search/search-flags';
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:46:      expect(searchHandler).toBeDefined();
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:49:        { name: 'searchHandler', ref: searchHandler },
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:50:        { name: 'hybridSearch', ref: hybridSearch },
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:64:          searchHandler.handleMemorySearch({ query: 'test search query' }),
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:92:          searchHandler.handleMemorySearch({ query: '' }),
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:117:          searchHandler.handleMemorySearch({ query: 'test', specFolder: 'specs/test-folder' }),
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:137:          searchHandler.handleMemorySearch({}),
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:152:      expect(typeof searchHandler.handleMemorySearch).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:153:      const fn = searchHandler.handleMemorySearch;
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:165:          searchHandler.handleMemorySearch({ concepts: ['single'] }),
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:183:          searchHandler.handleMemorySearch({ query: 'test', intent: 'fix_bug' }),
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:200:          searchHandler.handleMemorySearch({
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:222:          searchHandler.handleMemorySearch({
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:24:  runBM25Baseline,
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:26:  type BM25SearchFn,
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:27:  type BM25SearchResult,
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:28:  type BM25BaselineResult,
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:46:  hybridSearchEnhanced,
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:52:} from './search.js';
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:88:} from '../lib/search/folder-discovery.js';
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:89:export type { PerFolderDescription, LoadResult } from '../lib/search/folder-discovery.js';
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:132:export * as sessionBoost from '../lib/search/session-boost.js';
.opencode/skills/system-spec-kit/mcp_server/api/index.ts:133:export * as causalBoost from '../lib/search/causal-boost.js';
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:286:    const err = new MemoryError('E040', 'search failed', { q: 'test' });
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:287:    const resp = buildErrorResponse('memory_search', err);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:296:    const resp = buildErrorResponse('memory_search', err);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:302:    const resp = buildErrorResponse('memory_search', err);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:310:    const resp = buildErrorResponse('memory_search', err);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:311:    expect(resp.meta.tool).toBe('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:318:    const resp = buildErrorResponse('memory_search', err);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:328:  it('F7: Tool-specific hints included for memory_search + E001', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:330:    const resp = buildErrorResponse('memory_search', err);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:353:    const err = createErrorWithHint('E040', 'fail', {}, 'memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:469:  it('K2: Has memory_search, checkpoint_restore, memory_save', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:470:    expect('memory_search' in TOOL_SPECIFIC_HINTS).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:476:    const searchHints = TOOL_SPECIFIC_HINTS['memory_search'];
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:477:    expect(typeof searchHints).toBe('object');
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:478:    const codes = Object.keys(searchHints);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:480:    for (const [, hint] of Object.entries(searchHints)) {
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:492:  it('L1: Returns tool-specific hint for memory_search + E001', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:493:    const hint = getRecoveryHint('memory_search', 'E001');
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:495:      hint.hint.includes('Semantic search') || hint.hint.includes('search')
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:512:    const hint = getRecoveryHint('memory_search', 'E040');
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:524:  it('M1: Returns true for known tool+code (memory_search, E001)', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:525:    expect(hasSpecificHint('memory_search', 'E001')).toBe(true);
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:543:    const hints = getAvailableHints('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:550:    const hints = getAvailableHints('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/errors-comprehensive.vitest.ts:553:        hints['E001'].hint.includes('Semantic search') || hints['E001'].hint.includes('keyword')
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:11://     - Intent weights are NEVER applied to hybrid results (G2 double-weighting guard)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:29:// 4.  Intent weights          — non-hybrid search post-scoring adjustment
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:36:// Hybrid search already applies intent-aware scoring
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:37:// Internally (RRF / RSF fusion). Post-search intent weighting is
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:38:// Therefore ONLY applied for non-hybrid search types (vector,
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:39:// Multi-concept). Applying it to hybrid results would double-count.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:77:} from '../search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:94:import { resolveFusionIntentContract } from '../search-utils.js';
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:536: * Mirrors the `strengthenOnAccess` logic from the legacy memory-search
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:594: * Apply intent-based weights to search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:596: * G2 PREVENTION: This function is ONLY called for non-hybrid search types.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:597: * Hybrid search (RRF / RSF) already incorporates intent-weighted signals
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:598: * during fusion. Calling this on hybrid results would double-count intent.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:709: * @param query   - Original search query (used for learned trigger matching)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:848: * unintended write side-effects during read-only searches).
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:919:    // Adaptive signal capture must never block the core search pipeline.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:934: *   1.  Session boost      (hybrid only — working memory attention)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:936: *   2.  Causal boost       (hybrid only — graph-traversal amplification)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:941: *   4.  Intent weights     (non-hybrid only — G2 prevention)
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:979:  const isHybrid = config.searchType === 'hybrid';
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:982:  // Only for hybrid search type — session attention signals are most meaningful
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:983:  // When the full hybrid result set is available for ordering.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:1004:  // Uses computeRecencyScore (already imported but previously unused in hybrid path).
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:1044:  // Only for hybrid search type — causal graph traversal is seeded from the
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:1070:  // Appear in the co-activation graph. Matches V1 hybrid-search behavior.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:1223:  // G2 PREVENTION: Only apply for non-hybrid search types.
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:1224:  // Hybrid search (RRF / RSF) incorporates intent weighting during fusion —
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:1377:        searchType: config.searchType,
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-stats-edge.vitest.ts:4:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:30:    tool: 'memory_context',
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:37:    tool: 'memory_search',
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:43:    tool: 'memory_match_triggers',
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:176:  { tool: 'memory_context', handler: 'handleMemoryContext' },
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:177:  { tool: 'memory_search', handler: 'handleMemorySearch' },
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-input-validation.vitest.ts:179:  { tool: 'memory_match_triggers', handler: 'handleMemoryMatchTriggers' },
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-query-handler.vitest.ts:159:    // canonical vocabulary as code_graph_context (S2-matching).
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-query-handler.vitest.ts:321:  // and code_graph_query.
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:17:  generateCacheKey: vi.fn(() => 'gate-d-regression-4-stage-search-pipeline'),
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:23:vi.mock('../lib/search/pipeline/index.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:30:    _searchType: string,
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:60:vi.mock('../lib/search/artifact-routing.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:64:vi.mock('../lib/search/intent-classifier.js', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:77:import { handleMemorySearch } from '../handlers/memory-search';
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:83:describe('Gate D regression 13 — 4-stage search pipeline / RRF fusion', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:148:          searchType: 'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:183:      query: 'show the Gate D reader-ready 4-stage search pipeline fusion contract',
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-4-stage-search-pipeline.vitest.ts:205:    expect(stage1.searchType).toBe('hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/stage2b-enrichment.vitest.ts:8:vi.mock('../lib/search/anchor-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2b-enrichment.vitest.ts:12:vi.mock('../lib/search/validation-metadata', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/stage2b-enrichment.vitest.ts:16:import { executeStage2bEnrichment } from '../lib/search/pipeline/stage2b-enrichment';
.opencode/skills/system-spec-kit/mcp_server/tests/score-resolution-consistency.vitest.ts:8:import { resolveEffectiveScore } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/score-resolution-consistency.vitest.ts:9:import type { PipelineRow, Stage4ReadonlyRow } from '../lib/search/pipeline/types';
.opencode/skills/system-spec-kit/mcp_server/tests/score-resolution-consistency.vitest.ts:10:import { compareDeterministicRows } from '../lib/search/pipeline/ranking-contract';
.opencode/skills/system-spec-kit/mcp_server/tests/score-resolution-consistency.vitest.ts:11:import { extractScoringValue } from '../lib/search/pipeline/stage4-filter';
.opencode/skills/system-spec-kit/mcp_server/tests/description/fixtures/017-002-cluster-consumers.description.json:3:  "description": "Phase 017 Wave B child packet: 9 tasks / 30h across 3 parallel lanes consuming Wave A primitives. Lane B1 (Cluster B consumers, 12h, 4 tasks): T-CNS-02 research folder backfill, T-W1-CNS-05 continuity freshness validator, T-CGC-02 context.ts explicit error branch, T-RBD-03 design-intent comments. Lane B2 (Cluster D + Cluster E, 16h, 2 tasks): T-W1-CGC-03 5-sibling code-graph readiness propagation (atomic-ship or stub rollout), T-W1-HOK-01 Copilot compact-cache + session-prime (depends Wave A T-W1-HOK-02). Lane B3 (Cluster A + C + Standalone P1, 12h, 3 tasks): T-SCP-02 normalizer lint rule, T-SAN-01 + T-SAN-02 + T-SAN-03 NFKC unicode normalization + tests, T-PIN-RET-01 retry-exhaustion counter. Resolves FC-3 (research iteration folders metadata), FC-4 (6 code-graph handlers readiness vocabulary), FC-5 (Copilot compact-cache wiring), FC-6 (NFKC Gate 3 hardening), FC-8 (partial_causal_link_unresolved retry-exhaustion). Wave B gate: /spec_kit:deep-review :auto ×7 + validate.sh --strict on 017 folder.",
.opencode/skills/system-spec-kit/mcp_server/tests/description/fixtures/017-002-cluster-consumers.description.json:10:    "t-cns-02-research-folder-backfill",
.opencode/skills/system-spec-kit/mcp_server/tests/description/fixtures/017-002-cluster-consumers.description.json:25:    "r3-p1-002-research-folders-invisible",
.opencode/skills/system-spec-kit/mcp_server/tests/description/fixtures/017-002-cluster-consumers.description.json:37:    "fc-3-research-iteration-metadata",
.opencode/skills/system-spec-kit/mcp_server/api/README.md:3:description: "Stable import surface for eval, indexing, search, providers, storage, and selected architecture helpers."
.opencode/skills/system-spec-kit/mcp_server/api/README.md:34:| `eval.ts` | Ablation helpers, BM25 baseline helpers, ground-truth loading, and eval DB init |
.opencode/skills/system-spec-kit/mcp_server/api/README.md:36:| `search.ts` | Hybrid search init/search, FTS5 BM25 helpers, and `vectorIndex` namespace |
.opencode/skills/system-spec-kit/mcp_server/api/README.md:43:- Folder-discovery helpers from `lib/search/folder-discovery`.
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:3:// Covers: classifyEncodingIntent from lib/search/encoding-intent.ts
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:17:import { classifyEncodingIntent } from '../lib/search/encoding-intent';
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:18:import type { EncodingIntent } from '../lib/search/encoding-intent';
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:68:      'This is a memory about a decision we made regarding the search pipeline.',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:74:      'We evaluated BM25, vector search, and hybrid approaches. The hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:117:      'import { classifyEncodingIntent } from "../lib/search/encoding-intent";',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:162:      '  async search(query: string): Promise<Result[]> {',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:243:      'We decided to use the pipeline v2 architecture for the search system.',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:326:      '  async search(embedding: number[], limit: number): Promise<Row[]> {',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:345:      'After extensive evaluation of different search approaches, the team',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:350:      'independently. The retrieval stage handles both BM25 and vector',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:351:      'search, combining results via Reciprocal Rank Fusion.',
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:408:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:439:    const vectorIndex = await import('../lib/search/vector-index');
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage4-filter.ts:39:import { isTRMEnabled, isMultiQueryEnabled } from '../search-flags.js';
.opencode/skills/system-spec-kit/mcp_server/tests/review-fixes.vitest.ts:41:    const result = validateToolArgs('memory_search', {
.opencode/skills/system-spec-kit/mcp_server/tests/coverage-graph-status.vitest.ts:30:  loopType: 'research' as const,
.opencode/skills/system-spec-kit/mcp_server/tests/entity-linker.vitest.ts:16:} from '../lib/search/entity-linker';
.opencode/skills/system-spec-kit/mcp_server/tests/entity-linker.vitest.ts:22:} from '../lib/search/entity-linker';
.opencode/skills/system-spec-kit/mcp_server/tests/entity-linker.vitest.ts:202:      insertMemory(db, 10, 'specs/010-search');
.opencode/skills/system-spec-kit/mcp_server/tests/entity-linker.vitest.ts:203:      insertEntity(db, 10, 'BM25 Index');
.opencode/skills/system-spec-kit/mcp_server/tests/entity-linker.vitest.ts:208:      expect(entry.specFolders).toEqual(['specs/010-search']);
.opencode/skills/system-spec-kit/mcp_server/tests/cross-encoder.vitest.ts:3:import * as crossEncoder from '../lib/search/cross-encoder';
.opencode/skills/system-spec-kit/mcp_server/tests/graph-metadata-integration.vitest.ts:13:import { __testables as stage1Testables } from '../lib/search/pipeline/stage1-candidate-gen.js';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:29:  handle_memory_context,
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:37:} from '../lib/search/session-transition';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:114:  it('T004: deep mode has search strategy and 3500 token budget', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:116:    expect(deepMode.strategy).toBe('search');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:120:  it('T005: focused mode has intent-search strategy and 3000 token budget', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:122:    expect(focusedMode.strategy).toBe('intent-search');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:229:   T021-T030: handle_memory_context MAIN HANDLER TESTS
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:233:  it('T021: handle_memory_context is a function', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:280:  it('T029: handleMemoryContext is alias for handle_memory_context', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:281:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:434:  it('T038: Quick strategy differs from search strategies', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:460:  it('T041: Deep mode strategy is search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:461:    expect(CONTEXT_MODES.deep.strategy).toBe('search');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:515:  it('T051: Focused mode strategy is intent-search', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:516:    expect(CONTEXT_MODES.focused.strategy).toBe('intent-search');
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:848:  it('T101: handle_memory_context is exported', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:869:  it('T105: handleMemoryContext is same as handle_memory_context', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:870:    expect(handleMemoryContext).toBe(handle_memory_context);
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.vitest.ts:903:      meta: { tool: 'memory_search' }
.opencode/skills/system-spec-kit/mcp_server/tests/folder-relevance.vitest.ts:16:} from '../lib/search/folder-relevance';
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:39:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:47:vi.mock('../lib/search/hybrid-search', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:49:  hybridSearchEnhanced: mocks.mockHybridSearchEnhanced,
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:58:vi.mock('../lib/search/graph-search-fn', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:314:    it('T006-A10: ablation search forces all channels and wires graph search', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:335:      const searchFn = mocks.mockRunAblation.mock.calls[0]?.[0];
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:336:      expect(typeof searchFn).toBe('function');
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:338:      const results = await searchFn('graph-heavy query', new Set());
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:403:        queries: ['hybrid retrieval graph diagnosis'],
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:408:      expect(graphSearch).toHaveBeenCalledWith('hybrid retrieval graph diagnosis', { limit: 7 });
.opencode/skills/system-spec-kit/mcp_server/tests/handler-eval-reporting.vitest.ts:412:      expect(data.queriesUsed).toEqual(['hybrid retrieval graph diagnosis']);
.opencode/skills/system-spec-kit/mcp_server/tests/hook-session-start.vitest.ts:259:            '- CocoIndex: available',
.opencode/skills/system-spec-kit/mcp_server/tests/hook-session-start.vitest.ts:409:        recommendedAction: 'Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-verify.vitest.ts:62:  '../../../../../specs/system-spec-kit/026-graph-and-context-optimization/005-code-graph/006-code-graph-resilience-research/assets/code-graph-gold-queries.json',
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:4:// Feature catalog: Hybrid search pipeline
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:5:// Split from vector-index-store.ts — contains ALL query/search functions,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:30:  search_weights,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:159: * @param query_embedding - The query embedding to search with.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:165: * const rows = vector_search(queryEmbedding, { limit: 5, specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:168:export function vector_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:175:    console.warn('[vector-index] Vector search unavailable - sqlite-vec not loaded');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:307: * @param concept_embeddings - The concept embeddings to search with.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:313: * const rows = multi_concept_search([embA, embB], { limit: 8, specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:316:export function multi_concept_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:322:    console.warn('[vector-index] Multi-concept search unavailable - sqlite-vec not loaded');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:330:    throw new VectorIndexError('Multi-concept search requires 2-5 concepts', VectorIndexErrorCode.QUERY_FAILED);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:580: * Generates an embedding for a search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:581: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:606: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:610:export function keyword_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:618:    console.warn('[vector-index] keyword_search: invalid query, expected non-empty string');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:622:  const search_terms = query.toLowerCase().trim().split(/\s+/).filter(t => t.length >= 2);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:623:  if (search_terms.length === 0) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:624:    console.warn('[vector-index] keyword_search: no valid search terms after tokenization');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:647:    const searchable_text = [
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:654:    for (const term of search_terms) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:655:      if (searchable_text.includes(term)) {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:687: * Runs enriched vector search for a text query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:688: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:691: * @returns A promise that resolves to enriched search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:692: * @throws {VectorIndexError} Propagates vector-store initialization failures from the underlying search pipeline.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:695: * const results = await vector_search_enriched('sqlite vec mismatch', 10, { specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:698:export async function vector_search_enriched(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:710:  let search_method = 'vector';
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:714:    raw_results = vector_search(query_embedding, {
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:720:    console.warn('[vector-index] Falling back to keyword search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:721:    search_method = 'keyword';
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:722:    raw_results = keyword_search(query, { limit, specFolder }, database);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:737:    const similarity = search_method === 'vector'
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:752:      searchMethod: search_method,
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:759:    console.warn(`[vector-index] Enriched search took ${elapsed}ms (target <500ms)`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:770: * Runs enriched search across multiple concepts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:774: * @returns A promise that resolves to enriched search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:775: * @throws {VectorIndexError} When concept validation fails or the vector search pipeline cannot execute.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:778: * const results = await multi_concept_search_enriched(['sqlite', 'vector'], 10, { specFolder: 'specs/001-demo' });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:781:export async function multi_concept_search_enriched(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:789:    throw new VectorIndexError('Multi-concept search requires 2-5 concepts', VectorIndexErrorCode.QUERY_FAILED);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:800:        return await multi_concept_keyword_search(concepts.filter(c => typeof c === 'string'), limit, options);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:810:    console.warn('[vector-index] Falling back to keyword multi-concept search');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:811:    return await multi_concept_keyword_search(concepts.filter(c => typeof c === 'string'), limit, options);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:814:  const raw_results = multi_concept_search(concept_embeddings, { limit, specFolder, minSimilarity });
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:845:    console.warn(`[vector-index] Multi-concept search took ${elapsed}ms (target <500ms)`);
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:852: * Runs keyword search for multiple concepts.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:853: * @param concepts - The concept terms to search for.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:856: * @returns A promise that resolves to enriched search results.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:858:export async function multi_concept_keyword_search(
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:866:    console.warn('[vector-index] multi_concept_keyword_search: empty concepts array');
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:871:    keyword_search(concept, { limit: 100, specFolder })
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:920:      searchMethod: 'keyword',
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:929: * Parses quoted phrases from a search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:930: * @param query - The search query.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:931: * @returns The quoted search terms.
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:965:  const recency_weight = search_weights.smartRanking?.recencyWeight || 0.3;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:966:  const access_weight = search_weights.smartRanking?.accessWeight || 0.2;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:967:  const relevance_weight = search_weights.smartRanking?.relevanceWeight || 0.5;
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:1427:export { vector_search as vectorSearch };
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:1429:export { multi_concept_search as multiConceptSearch };
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:1435:export { keyword_search as keywordSearch };
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:1436:export { vector_search_enriched as vectorSearchEnriched };
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:1437:export { multi_concept_search_enriched as multiConceptSearchEnriched };
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:1438:export { multi_concept_keyword_search as multiConceptKeywordSearch };
.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:24:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:122:        memory_context: 'L1',
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:123:        memory_search: 'L2',
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:125:        memory_match_triggers: 'L2',
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:206:        { tool: 'memory_context', expected: '[L1:Orchestration]' },
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:207:        { tool: 'memory_search', expected: '[L2:Core]' },
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:233:      const result = mod.enhanceDescription('memory_context', 'Some description text');
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:239:        { tool: 'memory_search', desc: 'Search memories', prefix: '[L2:Core]' },
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:254:      expect(mod.enhanceDescription('memory_context', '')).toBe('[L1:Orchestration] ');
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:264:        { tool: 'memory_context', expected: 3500 },
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:265:        { tool: 'memory_search', expected: 3500 },
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:282:      expect(typeof mod.getTokenBudget('memory_context')).toBe('number');
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:292:      const info = expectLayerInfo(mod.getLayerInfo('memory_context'));
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:299:      expect(info.tools).toContain('memory_context');
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:303:      const info1 = mod.getLayerInfo('memory_context');
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:304:      const info2 = mod.getLayerInfo('memory_context');
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:313:      const info = expectLayerInfo(mod.getLayerInfo('memory_search'));
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:355:        search: ['L1', 'L2'],
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:369:      const result = mod.getRecommendedLayers('search');
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:384:      const taskTypes: TaskType[] = ['search', 'browse', 'modify', 'checkpoint', 'analyze', 'maintenance', 'default'];
.opencode/skills/system-spec-kit/mcp_server/tests/layer-definitions.vitest.ts:442:      const toolSamples = ['memory_context', 'memory_search', 'memory_list',
.opencode/skills/system-spec-kit/mcp_server/api/search.ts:5:// ARCH-1 stable re-export surface for search functionality.
.opencode/skills/system-spec-kit/mcp_server/api/search.ts:6:// Consumer scripts import from here instead of reaching into lib/search/.
.opencode/skills/system-spec-kit/mcp_server/api/search.ts:10:  hybridSearchEnhanced,
.opencode/skills/system-spec-kit/mcp_server/api/search.ts:13:} from '../lib/search/hybrid-search.js';
.opencode/skills/system-spec-kit/mcp_server/api/search.ts:18:} from '../lib/search/sqlite-fts.js';
.opencode/skills/system-spec-kit/mcp_server/api/search.ts:20:export * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/tests/code-graph-query-fallback-decision.vitest.ts:52:describe('code_graph_query fallbackDecision routing', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store.vitest.ts:12:} from '../lib/search/vector-index-store';
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:28:vi.mock('../lib/search/vector-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:70:vi.mock('../lib/search/bm25-index', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:98:vi.mock('../lib/search/search-flags', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:103:import * as vectorIndex from '../lib/search/vector-index';
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:104:import * as bm25Index from '../lib/search/bm25-index';
.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:562:  it('does not mutate parent BM25 document when all chunk inserts fail for an existing parent', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:7:import * as hybridSearch from '../lib/search/hybrid-search';
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:9:type HybridSearchOptions = NonNullable<Parameters<typeof hybridSearch.hybridSearchEnhanced>[2]>;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:10:type VectorSearchFn = NonNullable<Parameters<typeof hybridSearch.init>[1]>;
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:58:describe('Hybrid search feature flags', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:62:    hybridSearch.init(createMockDb(), mockVectorSearch);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:67:    await hybridSearch.hybridSearchEnhanced('test query', embedding, { limit: 3 } satisfies HybridSearchOptions);
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:74:    await hybridSearch.hybridSearchEnhanced('test query', embedding, { limit: 3 } satisfies HybridSearchOptions);
.opencode/skills/system-spec-kit/mcp_server/tests/p0-a-cross-runtime-tempdir-poisoning.vitest.ts:98:    const healthySpecFolder = 'specs/system-spec-kit/026-graph-and-context-optimization/016-foundational-runtime/001-initial-research';
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:192:        source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:217:      profile: 'research',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:224:        source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:237:        source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:244:      source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:275:        source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:306:        source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:318:        source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts:324:      source: 'semantic-search',
.opencode/skills/system-spec-kit/mcp_server/tests/session-bootstrap-gate-d.vitest.ts:74:        recommendedAction: 'Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/tests/session-bootstrap-gate-d.vitest.ts:89:    expect(messagingSurface).not.toContain('memory_context({ input: "resume previous work"');
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-cache.ts:4:// Shared result cache for LLM calls made during search.
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-cache.ts:48: * TTL-based in-process cache for LLM search results.
.opencode/skills/system-spec-kit/mcp_server/tests/local-reranker.vitest.ts:4:import { __testables } from '../lib/search/local-reranker';
.opencode/skills/system-spec-kit/mcp_server/tests/local-reranker.vitest.ts:6:type LocalRerankerModule = typeof import('../lib/search/local-reranker');
.opencode/skills/system-spec-kit/mcp_server/tests/local-reranker.vitest.ts:116:  return await import('../lib/search/local-reranker');
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:26:describe('db-state graph search wiring', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:40:    const hybridSearch = { init: vi.fn() };
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:48:      hybridSearch,
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:58:    expect(hybridSearch.init).toHaveBeenCalledWith(fakeDb, vectorIndex.vectorSearch, fakeGraphFn);
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:80:      const hybridSearch = { init: vi.fn() };
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:88:        hybridSearch,
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:120:    const hybridSearch = { init: vi.fn() };
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:128:      hybridSearch,
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:158:    const hybridSearch = { init: vi.fn() };
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:167:      hybridSearch,
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:181:    expect(hybridSearch.init).toHaveBeenCalledWith(reboundDb, vectorIndex.vectorSearch, null);
.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:210:      hybridSearch: { init: vi.fn() },
.opencode/skills/system-spec-kit/mcp_server/api/eval.ts:25:  runBM25Baseline,
.opencode/skills/system-spec-kit/mcp_server/api/eval.ts:27:  type BM25SearchFn,
.opencode/skills/system-spec-kit/mcp_server/api/eval.ts:28:  type BM25SearchResult,
.opencode/skills/system-spec-kit/mcp_server/api/eval.ts:29:  type BM25BaselineResult,
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:8:} from '../formatters/search-results';
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:14:  searchType?: string;
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:82:    const response = await formatSearchResults([createMockResult()], 'hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:86:    expect(envelope.meta.tool).toBe('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:92:    const response = await formatSearchResults([createMockResult()], 'hybrid');
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:104:      'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:188:      'hybrid',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-lineage-state.vitest.ts:4:import { createSchema, ensureSchemaVersion, validateLineageSchemaSupport } from '../lib/search/vector-index-schema';
.opencode/skills/system-spec-kit/mcp_server/tests/schema-migration.vitest.ts:6:import * as vectorIndex from '../lib/search/vector-index.js';
.opencode/skills/system-spec-kit/mcp_server/api/indexing.ts:22:import { initHybridSearch, vectorIndex } from './search.js';
.opencode/skills/system-spec-kit/mcp_server/api/indexing.ts:42:    hybridSearch: { init: initHybridSearch },
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:10:} from '../lib/search/query-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:17:} from '../lib/search/dynamic-token-budget';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:25:} from '../lib/search/intent-classifier';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:43:} from '../lib/search/channel-representation';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:74:} from '../lib/search/confidence-truncation';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:167:      const intent = classifyIntent('fix the memory search bug');
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:287:        'how does the cross encoder reranker work with the hybrid search pipeline and vector index',
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:578:      const query = 'fix the memory search scoring bug in hybrid pipeline';
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:594:      // Step 5: Fuse search results via RRF
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:596:        makeRrfItem(1, { title: 'Memory search fix' }),
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:598:        makeRrfItem(3, { title: 'Hybrid search' }),
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:603:        makeRrfItem(1, { title: 'Memory search fix' }),
.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:632:      // Simulate search results with different attributes
.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:50:    const response = buildErrorResponse('memory_search', error);
.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:68:    const response = buildErrorResponse('memory_search', error);
.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:83:    const response = buildErrorResponse('memory_search', error);
.opencode/skills/system-spec-kit/mcp_server/tests/error-sanitization.vitest.ts:90:  it('maps non-search tools to domain-specific default error codes', () => {
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:18:  | 'research'
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:23:  /** Weight for semantic (vector) search component, 0-1 */
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:25:  /** Weight for keyword (BM25) search component, 0-1 */
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:109:  research: {
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:110:    artifactClass: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:142:  { pattern: /research\.md$/i, artifactClass: 'research' },
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:188:    artifactClass: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:189:    keywords: ['research', 'investigation', 'analysis', 'findings', 'study', 'evaluation', 'search', 'retrieval', 'pipeline', 'indexing', 'embedding', 'vector', 'semantic'],
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:190:    patterns: [/research\.md/i, /research\s+(?:findings|results|notes)/i],
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:209:  understand: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:215:  security_audit: 'research',
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:334: * Apply routing-based weight adjustments to search results.
.opencode/skills/system-spec-kit/mcp_server/tests/graph-payload-validator.vitest.ts:163:        'code_graph_query outline payload rejects collapsed scalar fields: trust.',
.opencode/skills/system-spec-kit/mcp_server/tests/graph-payload-validator.vitest.ts:212:      isCocoIndexAvailable: vi.fn(() => true),
.opencode/skills/system-spec-kit/mcp_server/tests/graph-payload-validator.vitest.ts:234:        recommendedAction: 'Use code_graph_query for structural lookups.',
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-schema-migration-refinements.vitest.ts:10:} from '../lib/search/vector-index-schema';
.opencode/skills/system-spec-kit/mcp_server/tests/mutation-hooks.vitest.ts:36:vi.mock('../lib/search/graph-search-fn', () => ({
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:2:// 1. TEST — BM25 BASELINE
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:13:// T008.8  — runBM25Baseline: runs with mocked search function
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:14:// T008.9  — runBM25Baseline: respects queryLimit config option
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:15:// T008.10 — runBM25Baseline: skipHardNegatives reduces query count
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:16:// T008.11 — runBM25Baseline: returns well-structured BM25BaselineResult
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:17:// T008.12 — runBM25Baseline: disables non-BM25 channels (only calls searchFn)
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:40:  runBM25Baseline,
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:41:  type BM25BaselineResult,
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:42:  type BM25SearchResult,
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:76:/** Build a mock search function that returns `count` deterministic results. */
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:77:function makeMockSearchFn(count: number = 5): (query: string, limit: number) => BM25SearchResult[] {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:88:/** Build a mock result object representing a complete BM25 baseline run. */
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:89:function makeMockResult(mrr5: number): BM25BaselineResult {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:107:describe('T008: BM25 Contingency Decision Matrix', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:163:describe('T008: BM25 Relative Contingency Decision', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:166:    // BM25=0.72, hybrid=0.80 → ratio=0.90 → PAUSE
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:171:    expect(result.hybridMRR).toBe(0.80);
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:176:    // BM25=0.40, hybrid=0.70 → ratio=0.571 → RATIONALIZE
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:184:    // BM25=0.20, hybrid=0.75 → ratio=0.267 → PROCEED
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:193:    // BM25=0.40, hybrid=0.50 → ratio=0.80 exactly
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:200:    // BM25=0.25, hybrid=0.50 → ratio=0.50 exactly
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:206:  it('T008.18: hybridMRR=0 → safe fallback to PROCEED', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:224:    expect(result.hybridMRR).toBeUndefined();
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:387:   TESTS: runBM25Baseline
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:390:describe('T008: runBM25Baseline — Runner Integration', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:392:  it('T008.8: runs with a mocked search function and returns well-structured result', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:394:    const result = await runBM25Baseline(mockSearch, { queryLimit: 10 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:410:    const result = await runBM25Baseline(mockSearch, { queryLimit: 7 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:420:    const withHardNeg = await runBM25Baseline(mockSearch, { skipHardNegatives: false });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:421:    const withoutHardNeg = await runBM25Baseline(mockSearch, { skipHardNegatives: true });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:428:  it('T008.11: returns well-structured BM25BaselineResult with contingency decision', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:430:    const result = await runBM25Baseline(mockSearch, { queryLimit: 5 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:440:  it('T008.12: only invokes the injected searchFn — no side-channel calls', async () => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:442:    // To call vector, graph, or trigger search paths (those are controlled by
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:443:    // The caller who must disable them before passing the search function).
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:445:    const trackingSearch = (query: string, limit: number): BM25SearchResult[] => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:450:    const result = await runBM25Baseline(trackingSearch, { queryLimit: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:462:    const result = await runBM25Baseline(mockSearch, { queryLimit: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:477:    const mockSearch = (query: string, _limit: number): BM25SearchResult[] => {
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:489:    const baseline = await runBM25Baseline(mockSearch, { queryLimit: 3 });
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:490:    const withKOverride = await runBM25Baseline(mockSearch, { queryLimit: 3, k: 1 });
.opencode/skills/system-spec-kit/mcp_server/tests/query-flow-tracker.vitest.ts:122:  it('records the packet flow of search citation, follow-on tool use, and reformulation in the ledger', () => {
.opencode/skills/system-spec-kit/mcp_server/tests/session-manager-extended.vitest.ts:626:      expect(md).toContain('memory_search');
.opencode/skills/system-spec-kit/mcp_server/tests/fixtures/similarity-test-cases.json:81:      "a": "Use vector embeddings for search",
.opencode/skills/system-spec-kit/mcp_server/tests/fixtures/similarity-test-cases.json:82:      "b": "Semantic search with embeddings",
.opencode/skills/system-spec-kit/mcp_server/tests/fixtures/contradiction-pairs.json:64:      "a": "Prefer semantic search for code",
.opencode/skills/system-spec-kit/mcp_server/tests/fixtures/contradiction-pairs.json:65:      "b": "Use semantic search when available",
.opencode/skills/system-spec-kit/mcp_server/tests/fixtures/sample-memories.json:77:      "content": "Vector embeddings use 384 dimensions for semantic search",
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:11:} from '../lib/search/tfidf-summarizer';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:18:} from '../lib/search/memory-summaries';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:290:      'The system uses vector embeddings for semantic search.',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:293:      'Retrieval pipelines combine multiple search channels.',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:326:      'Alpha sentence about search pipelines and indexing strategies.',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:372:    const content = 'The system provides comprehensive search capabilities for memory retrieval.';
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:387:      'The dimensionality of embeddings affects search precision.',
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:451:    await generateAndStoreSummary(db, 1, 'The search pipeline retrieves documents using vector similarity over embedding space.', mockEmbeddingFn);
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:453:    await generateAndStoreSummary(db, 3, 'The retrieval system uses semantic search and vector embeddings for matching.', mockEmbeddingFn);
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:455:    // Query with embedding similar to memory 1 and 3 (search/retrieval topic)
.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:456:    const queryEmb = await mockEmbeddingFn('search pipeline vector similarity retrieval');
.opencode/skills/system-spec-kit/mcp_server/tests/shadow-scoring-holdout.vitest.ts:235:        ['q4', 'research'], ['q5', 'research'], ['q6', 'research'],

exec
/bin/zsh -lc "rg --files .opencode/skills/system-spec-kit/mcp_server .opencode/skills/mcp-coco-index | rg '(search|context|code-graph|cocoindex|query|retrieval|rank|fusion|trigger)'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/schema.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/daemon.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/project.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/__main__.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/settings.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/indexer.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/cli.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/shared.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/__init__.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/client.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/protocol.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/_version.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/query.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/LICENSE
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/config.py
.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py
.opencode/skills/system-spec-kit/mcp_server/context-server.ts
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/001-query-intent-semantic-routing.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/002-hybrid-query-merges-results.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/07--code-graph-integration/003-session-resume-includes-cocoindex.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/003-language-filter-multi.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/004-path-filter.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/001-basic-semantic-search.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/005-combined-filters.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/007-no-refresh-search.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/006-result-limit.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/008-concurrent-refresh-race.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/02--mcp-search-tool/002-language-filter-single.md
.opencode/skills/mcp-coco-index/manual_testing_playbook/01--core-cli-commands/004-cli-search-with-filters.md
.opencode/skills/mcp-coco-index/references/search_patterns.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/fusion.ts
.opencode/skills/system-spec-kit/mcp_server/api/search.ts
.opencode/skills/system-spec-kit/mcp_server/plugin_bridges/spec-kit-compact-code-graph-bridge.mjs
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts
.opencode/skills/system-spec-kit/mcp_server/configs/search-weights.json
.opencode/skills/system-spec-kit/mcp_server/lib/session/context-metrics.ts
.opencode/skills/system-spec-kit/mcp_server/lib/context/caller-context.ts
.opencode/skills/system-spec-kit/mcp_server/lib/context/opencode-transport.ts
.opencode/skills/system-spec-kit/mcp_server/lib/context/publication-gate.ts
.opencode/skills/system-spec-kit/mcp_server/lib/context/README.md
.opencode/skills/system-spec-kit/mcp_server/lib/context/shared-payload.ts
.opencode/skills/system-spec-kit/mcp_server/tools/context-tools.ts
.opencode/skills/system-spec-kit/mcp_server/tests/adaptive-ranking-e2e.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/adaptive-ranking.ts
.opencode/skills/system-spec-kit/mcp_server/lib/telemetry/retrieval-telemetry.ts
.opencode/skills/system-spec-kit/mcp_server/tests/usage-weighted-ranking.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/memory-context.resume-gate-d.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/auto-promotion.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/learned-feedback.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-relevance.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/hyde.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/confidence-truncation.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-types.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-flags.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/feedback-denylist.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-boost.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/evidence-gap-detector.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/surrogate-storage.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-calibration.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/reranker.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-lifecycle.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/encoding-intent.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/memory-summaries.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/validation-metadata.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-surrogates.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/anchor-metadata.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-decomposer.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/spec-folder-hierarchy.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-router.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-expander.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/retrieval-directives.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-utils.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/tfidf-summarizer.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/dynamic-token-budget.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/confidence-scoring.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-types.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/causal-boost.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/deterministic-extractor.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-transition.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/query-classifier.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-state.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-reformulation.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/channel-representation.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/folder-discovery.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/community-search.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/chunk-reassembly.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-impl.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/fsrs.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/channel-enforcement.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/progressive-disclosure.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/local-reranker.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts
.opencode/skills/system-spec-kit/mcp_server/tests/search-limits-scoring.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/trigger-setAttentionScore.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/unit-rrf-fusion.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/query-surrogates.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/ranking-contract.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/index.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/types.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/orchestrator.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2b-enrichment.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage4-filter.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/llm-cache.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts
.opencode/skills/system-spec-kit/mcp_server/tests/query-router.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/lib/storage/learned-triggers-schema.ts
.opencode/skills/system-spec-kit/mcp_server/tests/trigger-extractor.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/query-expander.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/lib/feedback/rank-metrics.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/bench/code-graph-parse-latency.bench.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/bench/code-graph-query-latency.bench.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/bench/code-graph-query-latency.baseline.json
.opencode/skills/system-spec-kit/mcp_server/tests/reranker.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/handlers/skill-graph/query.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/feature_catalog/04--scorer-fusion/06-weights-config.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/feature_catalog/04--scorer-fusion/01-five-lane-fusion.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/feature_catalog/04--scorer-fusion/02-projection.md
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/query.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/feature_catalog/04--scorer-fusion/05-ablation.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/feature_catalog/04--scorer-fusion/04-attribution.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/feature_catalog/04--scorer-fusion/03-ambiguity.md
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-db.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-result-adapter.ts
.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-context.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/manual_testing_playbook/08--scorer-fusion/005-ablation.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/manual_testing_playbook/08--scorer-fusion/001-five-lane-fusion.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/manual_testing_playbook/08--scorer-fusion/002-projection.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/manual_testing_playbook/08--scorer-fusion/003-ambiguity.md
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/manual_testing_playbook/08--scorer-fusion/004-lane-attribution.md
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/gold-query-verifier.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-trigger-perf-benchmark.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/code_graph/tools/code-graph-tools.ts
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.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/assets/code-graph-gold-queries.json
.opencode/skills/system-spec-kit/mcp_server/tests/trigger-matcher.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/search-archival.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/search-results-format.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-search.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-triggers.vitest.ts

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts | sed -n '1,260p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	// ───────────────────────────────────────────────────────────────
     2	// MODULE: Memory Search
     3	// ───────────────────────────────────────────────────────────────
     4	/* ───────────────────────────────────────────────────────────────
     5	   1. DEPENDENCIES
     6	──────────────────────────────────────────────────────────────── */
     7	
     8	import * as toolCache from '../lib/cache/tool-cache.js';
     9	import * as causalEdges from '../lib/storage/causal-edges.js';
    10	import * as sessionManager from '../lib/session/session-manager.js';
    11	import * as intentClassifier from '../lib/search/intent-classifier.js';
    12	// TierClassifier, crossEncoder imports removed — only used by legacy V1 pipeline.
    13	import { isSessionBoostEnabled, isCausalBoostEnabled, isCommunitySearchFallbackEnabled, isDualRetrievalEnabled, isIntentAutoProfileEnabled } from '../lib/search/search-flags.js';
    14	import { searchCommunities } from '../lib/search/community-search.js';
    15	// 4-stage pipeline architecture
    16	import { executePipeline } from '../lib/search/pipeline/index.js';
    17	import type { PipelineConfig, PipelineResult } from '../lib/search/pipeline/index.js';
    18	import type { IntentWeightsConfig } from '../lib/search/pipeline/types.js';
    19	import { initConsumptionLog, logConsumptionEvent } from '../lib/telemetry/consumption-logger.js';
    20	import * as retrievalTelemetry from '../lib/telemetry/retrieval-telemetry.js';
    21	// Artifact-class routing (spec/plan/tasks/checklist/memory)
    22	import { getStrategyForQuery } from '../lib/search/artifact-routing.js';
    23	// Chunk reassembly (extracted from this file)
    24	import { collapseAndReassembleChunkResults } from '../lib/search/chunk-reassembly.js';
    25	// Search utilities (extracted from this file)
    26	import {
    27	  filterByMinQualityScore,
    28	  resolveQualityThreshold,
    29	  buildCacheArgs,
    30	  resolveRowContextType,
    31	  resolveArtifactRoutingQuery,
    32	  applyArtifactRouting,
    33	} from '../lib/search/search-utils.js';
    34	// CacheArgsInput used internally by buildCacheArgs (lib/search/search-utils.ts)
    35	// Eval channel tracking (extracted from this file)
    36	import {
    37	  collectEvalChannelsFromRow,
    38	  buildEvalChannelPayloads,
    39	  summarizeGraphWalkDiagnostics,
    40	} from '../lib/telemetry/eval-channel-tracking.js';
    41	import type { EvalChannelPayload } from '../lib/telemetry/eval-channel-tracking.js';
    42	
    43	// Eval logger — fail-safe, no-op when SPECKIT_EVAL_LOGGING !== "true"
    44	import { logSearchQuery, logChannelResult, logFinalResult } from '../lib/eval/eval-logger.js';
    45	import {
    46	  logFeedbackEvents,
    47	  isImplicitFeedbackLogEnabled,
    48	} from '../lib/feedback/feedback-ledger.js';
    49	import type { FeedbackEvent } from '../lib/feedback/feedback-ledger.js';
    50	import { trackQueryAndDetect, logResultCited } from '../lib/feedback/query-flow-tracker.js';
    51	
    52	// Core utilities
    53	import { checkDatabaseUpdated, isEmbeddingModelReady, waitForEmbeddingModel } from '../core/index.js';
    54	import { validateQuery, requireDb, toErrorMessage } from '../utils/index.js';
    55	
    56	// Response envelope + formatters
    57	import { createMCPErrorResponse, createMCPSuccessResponse } from '../lib/response/envelope.js';
    58	import { formatSearchResults } from '../formatters/index.js';
    59	
    60	// Shared handler types
    61	import type { MCPResponse, IntentClassification } from './types.js';
    62	
    63	// Retrieval trace contracts (C136-08)
    64	import { createTrace } from '@spec-kit/shared/contracts/retrieval-trace';
    65	import { buildAdaptiveShadowProposal } from '../lib/cognitive/adaptive-ranking.js';
    66	import { normalizeScopeContext } from '../lib/governance/scope-governance.js';
    67	import {
    68	  attachSessionTransitionTrace,
    69	  type SessionTransitionTrace,
    70	} from '../lib/search/session-transition.js';
    71	
    72	// REQ-D5-003: Mode-Aware Response Shape
    73	import {
    74	  applyProfileToEnvelope,
    75	  isResponseProfileEnabled,
    76	} from '../lib/response/profile-formatters.js';
    77	import {
    78	  buildProgressiveResponse,
    79	  extractSnippets,
    80	  isProgressiveDisclosureEnabled,
    81	  resolveCursor,
    82	} from '../lib/search/progressive-disclosure.js';
    83	import {
    84	  SPEC_DOCUMENT_FILENAMES,
    85	  canClassifyAsSpecDocument,
    86	  normalizeSpecPath,
    87	} from '../lib/config/spec-doc-paths.js';
    88	import {
    89	  getLastLexicalCapabilitySnapshot,
    90	  resetLastLexicalCapabilitySnapshot,
    91	} from '../lib/search/sqlite-fts.js';
    92	import type { LexicalCapabilitySnapshot } from '../lib/search/sqlite-fts.js';
    93	import { evaluatePublicationGate } from '../lib/context/publication-gate.js';
    94	import {
    95	  deduplicateResults as deduplicateWithSessionState,
    96	  isSessionRetrievalStateEnabled,
    97	  manager as retrievalSessionStateManager,
    98	  refineForGoal,
    99	} from '../lib/search/session-state.js';
   100	
   101	// Type imports for casting
   102	import type { IntentType, IntentWeights as IntentClassifierWeights } from '../lib/search/intent-classifier.js';
   103	import type { RawSearchResult } from '../formatters/index.js';
   104	// RoutingResult, WeightedResult — now used internally by lib/search/search-utils.ts
   105	
   106	// Feature catalog: Semantic and lexical search (memory_search)
   107	// Feature catalog: Hybrid search pipeline
   108	// Feature catalog: 4-stage pipeline architecture
   109	// Feature catalog: Quality-aware 3-tier search fallback
   110	
   111	
   112	/* ───────────────────────────────────────────────────────────────
   113	   2. TYPES
   114	──────────────────────────────────────────────────────────────── */
   115	
   116	/**
   117	 * Internal search result row — enriched DB row used within this handler.
   118	 * NOT the same as the canonical SearchResult in shared/types.ts.
   119	 * Self-contained: uses local types instead of the deprecated MemoryRow/MemoryRecord shapes.
   120	 * This can migrate to MemoryDbRow & Record<string, unknown> later without changing the handler contract.
   121	 */
   122	interface MemorySearchRow extends Record<string, unknown> {
   123	  id: number;
   124	  similarity?: number;
   125	  importance_tier?: string;
   126	  contextType?: string;
   127	  context_type?: string;
   128	  attentionScore?: number;
   129	  retrievability?: number;
   130	  stability?: number;
   131	  last_review?: string | null;
   132	  created_at?: string;
   133	  last_accessed?: number;
   134	  content?: string;
   135	  memoryState?: string;
   136	  file_path?: string;
   137	  parent_id?: number | null;
   138	  chunk_index?: number | null;
   139	  chunk_label?: string | null;
   140	  isChunk?: boolean;
   141	  parentId?: number | null;
   142	  chunkIndex?: number | null;
   143	  chunkLabel?: string | null;
   144	  chunkCount?: number | null;
   145	  contentSource?: 'reassembled_chunks' | 'file_read_fallback';
   146	  precomputedContent?: string;
   147	}
   148	
   149	interface DedupResult {
   150	  results: MemorySearchRow[];
   151	  dedupStats: Record<string, unknown>;
   152	}
   153	
   154	interface SearchCachePayload {
   155	  summary: string;
   156	  data: Record<string, unknown>;
   157	  hints: string[];
   158	}
   159	
   160	type SessionAwareResult = Record<string, unknown> & {
   161	  id: number | string;
   162	  score?: number;
   163	  content?: string;
   164	};
   165	
   166	type CanonicalSourceKind = 'spec_doc' | 'continuity' | 'constitutional';
   167	
   168	interface CanonicalSourceStats {
   169	  retained: number;
   170	  dropped: number;
   171	  bySourceKind: Record<CanonicalSourceKind, number>;
   172	}
   173	
   174	const CONTINUITY_ANCHOR_ID = '_memory.continuity';
   175	const CANONICAL_READER_CACHE_VERSION = 'gate-d-reader-ready-v1';
   176	const CANONICAL_SPEC_DOC_DOCUMENT_TYPES = new Set([
   177	  'spec',
   178	  'plan',
   179	  'tasks',
   180	  'checklist',
   181	  'decision_record',
   182	  'implementation_summary',
   183	  'research',
   184	  'handover',
   185	  'graph_metadata',
   186	  'spec_doc',
   187	]);
   188	const NON_CANONICAL_DOCUMENT_TYPES = new Set([
   189	  'memory',
   190	  'scratch',
   191	]);
   192	
   193	function normalizeDocumentType(value: unknown): string | null {
   194	  if (typeof value !== 'string') {
   195	    return null;
   196	  }
   197	  const normalized = value.trim().toLowerCase();
   198	  return normalized.length > 0 ? normalized : null;
   199	}
   200	
   201	function resolveAnchorId(row: Record<string, unknown>): string | null {
   202	  const value = row.anchor_id ?? row.anchorId;
   203	  return typeof value === 'string' && value.trim().length > 0
   204	    ? value.trim()
   205	    : null;
   206	}
   207	
   208	function resolveFilePath(row: Record<string, unknown>): string | null {
   209	  const value = row.file_path ?? row.filePath;
   210	  return typeof value === 'string' && value.trim().length > 0
   211	    ? value
   212	    : null;
   213	}
   214	
   215	function resolveCanonicalSourceKind(row: Record<string, unknown>): CanonicalSourceKind | null {
   216	  const documentType = normalizeDocumentType(row.document_type ?? row.documentType);
   217	  const importanceTier = normalizeDocumentType(row.importance_tier ?? row.importanceTier);
   218	  const anchorId = resolveAnchorId(row);
   219	
   220	  if (importanceTier === 'constitutional' || documentType === 'constitutional') {

 succeeded in 0ms:
     1	// ───────────────────────────────────────────────────────────────
     2	// MODULE: Hybrid Search
     3	// ───────────────────────────────────────────────────────────────
     4	// Combines vector, FTS, and BM25 search with fallback
     5	
     6	// 1. IMPORTS
     7	
     8	// Local
     9	import { getIndex, isBm25Enabled } from './bm25-index.js';
    10	import { fuseResultsMulti } from '@spec-kit/shared/algorithms/rrf-fusion';
    11	import { adaptiveFuse, getAdaptiveWeights, isAdaptiveFusionEnabled } from '@spec-kit/shared/algorithms/adaptive-fusion';
    12	import { CO_ACTIVATION_CONFIG, spreadActivation } from '../cognitive/co-activation.js';
    13	import { applyMMR } from '@spec-kit/shared/algorithms/mmr-reranker';
    14	import { INTENT_LAMBDA_MAP, classifyIntent } from './intent-classifier.js';
    15	import { fts5Bm25Search } from './sqlite-fts.js';
    16	import { DEGREE_CHANNEL_WEIGHT } from './graph-search-fn.js';
    17	import {
    18	  isMMREnabled,
    19	  isCrossEncoderEnabled,
    20	  isLocalRerankerEnabled,
    21	  isSearchFallbackEnabled,
    22	  isDocscoreAggregationEnabled,
    23	  isDegreeBoostEnabled,
    24	  isContextHeadersEnabled,
    25	} from './search-flags.js';
    26	import { rerankLocal } from './local-reranker.js';
    27	import { computeDegreeScores } from './graph-search-fn.js';
    28	import type { GraphSearchFn } from './search-types.js';
    29	
    30	// Feature catalog: Hybrid search pipeline
    31	
    32	export type { GraphSearchFn } from './search-types.js';
    33	
    34	import { routeQuery } from './query-router.js';
    35	import { isComplexityRouterEnabled } from './query-classifier.js';
    36	import { enforceChannelRepresentation } from './channel-enforcement.js';
    37	import {
    38	  truncateByConfidence,
    39	  isConfidenceTruncationEnabled,
    40	  DEFAULT_MIN_RESULTS,
    41	  GAP_THRESHOLD_MULTIPLIER,
    42	} from './confidence-truncation.js';
    43	import {
    44	  getDynamicTokenBudget,
    45	  isDynamicTokenBudgetEnabled,
    46	  DEFAULT_TOKEN_BUDGET_CONFIG,
    47	} from './dynamic-token-budget.js';
    48	import { resolveFusionIntentContract } from './search-utils.js';
    49	import { ensureDescriptionCache, getSpecsBasePaths } from './folder-discovery.js';
    50	import {
    51	  isFolderScoringEnabled,
    52	  lookupFolders,
    53	  computeFolderRelevanceScores,
    54	  enrichResultsWithFolderScores,
    55	  twoPhaseRetrieval,
    56	} from './folder-relevance.js';
    57	
    58	import { collapseAndReassembleChunkResults } from '../scoring/mpab-aggregation.js';
    59	
    60	// Type-only
    61	import type Database from 'better-sqlite3';
    62	import type { SpreadResult } from '../cognitive/co-activation.js';
    63	import type { MMRCandidate } from '@spec-kit/shared/algorithms/mmr-reranker';
    64	import type { FusionResult } from '@spec-kit/shared/algorithms/rrf-fusion';
    65	import type { ChannelName } from './query-router.js';
    66	import type { EnforcementResult } from './channel-enforcement.js';
    67	import type { TruncationResult } from './confidence-truncation.js';
    68	
    69	// 2. INTERFACES
    70	
    71	type VectorSearchFn = (
    72	  embedding: Float32Array | number[],
    73	  options: Record<string, unknown>
    74	) => Array<Record<string, unknown>>;
    75	
    76	interface HybridSearchOptions {
    77	  limit?: number;
    78	  specFolder?: string;
    79	  minSimilarity?: number;
    80	  useBm25?: boolean;
    81	  useFts?: boolean;
    82	  useVector?: boolean;
    83	  useGraph?: boolean;
    84	  includeArchived?: boolean;
    85	  includeContent?: boolean;
    86	  /**
    87	   * Evaluation-only mode.
    88	   * When true, preserve the requested top-K window by bypassing confidence
    89	   * truncation and token-budget truncation without changing live defaults.
    90	   */
    91	  evaluationMode?: boolean;
    92	  /** Classified query intent for adaptive fusion weight selection (e.g. 'understand', 'fix_bug'). */
    93	  intent?: string;
    94	  /** Optional trigger phrases for query-classifier trigger-match routing path. */
    95	  triggerPhrases?: string[];
    96	  /**
    97	   * Internal fallback override: when true, bypass complexity routing and
    98	   * enable all retrieval channels for this search call.
    99	   */
   100	  forceAllChannels?: boolean;
   101	  /**
   102	   * Internal raw-candidate mode used by the Stage 1 pipeline.
   103	   * When true, stop after channel collection and return pre-fusion candidates.
   104	   */
   105	  skipFusion?: boolean;
   106	  /**
   107	   * Internal pipeline handoff mode.
   108	   * When true, return immediately after adaptive/RRF fusion so Stage 2/3 can
   109	   * apply the remaining pipeline scoring and aggregation steps.
   110	   */
   111	  stopAfterFusion?: boolean;
   112	}
   113	
   114	interface HybridSearchResult {
   115	  id: number | string;
   116	  /**
   117	   * Normalized relevance score (0-1). Semantics depend on `source`:
   118	   * - `'vector'` — cosine similarity from sqlite-vec (normalized from 0-100 to 0-1)
   119	   * - `'bm25'` — BM25 term-frequency relevance (min-max normalized per source group)
   120	   * - `'fts'` — FTS5 rank score (absolute value, min-max normalized per source group)
   121	   * - `'graph'` — graph traversal relevance
   122	   *
   123	   * After hybrid merge, all source scores are min-max normalized to 0-1 within
   124	   * their source group to ensure fair cross-method comparison (see P3-02 fix).
   125	   */
   126	  score: number;
   127	  source: string;
   128	  title?: string;
   129	  [key: string]: unknown;
   130	}
   131	
   132	/** Non-enumerable shadow metadata attached to result arrays via Object.defineProperty. */
   133	interface ShadowMetaArray {
   134	  _s4shadow?: unknown;
   135	  _s4attribution?: unknown;
   136	  _degradation?: unknown;
   137	}
   138	
   139	/** Normalize a fused RRF result to the HybridSearchResult contract. */
   140	function toHybridResult(result: FusionResult): HybridSearchResult {
   141	  const sourceCandidate = (result as { source?: unknown }).source;
   142	  const primarySource = result.sources[0] ?? 'hybrid';
   143	  const scoreCandidate = (result as { score?: unknown }).score;
   144	
   145	  return {
   146	    ...result,
   147	    id: result.id,
   148	    score: typeof scoreCandidate === 'number' ? scoreCandidate : result.rrfScore,
   149	    source: typeof sourceCandidate === 'string' ? sourceCandidate : primarySource,
   150	  };
   151	}
   152	
   153	// 3. SPRINT 3 PIPELINE METADATA
   154	
   155	/**
   156	 * Optional metadata about pipeline stages attached to enhanced search results.
   157	 * Only populated when the corresponding feature flags are enabled.
   158	 */
   159	interface Sprint3PipelineMeta {
   160	  /** Query complexity routing result (SPECKIT_COMPLEXITY_ROUTER). */
   161	  routing?: {
   162	    tier: string;
   163	    channels: string[];
   164	    skippedChannels: string[];
   165	    featureFlagEnabled: boolean;
   166	    confidence: string;
   167	    features: Record<string, unknown>;
   168	  };
   169	  /** Channel enforcement result (SPECKIT_CHANNEL_MIN_REP). */
   170	  enforcement?: { applied: boolean; promotedCount: number; underRepresentedChannels: string[] };
   171	  /** Confidence truncation result (SPECKIT_CONFIDENCE_TRUNCATION). */
   172	  truncation?: {
   173	    truncated: boolean;
   174	    originalCount: number;
   175	    truncatedCount: number;
   176	    medianGap: number;
   177	    cutoffGap: number;
   178	    cutoffIndex: number;
   179	    thresholdMultiplier: number;
   180	    minResultsGuaranteed: number;
   181	    featureFlagEnabled: boolean;
   182	  };
   183	  /** Dynamic token budget result (SPECKIT_DYNAMIC_TOKEN_BUDGET). */
   184	  tokenBudget?: {
   185	    tier: string;
   186	    budget: number;
   187	    applied: boolean;
   188	    featureFlagEnabled: boolean;
   189	    configValues: Record<string, number>;
   190	    headerOverhead: number;
   191	    adjustedBudget: number;
   192	  };
   193	}
   194	
   195	// 4. PI-A2: DEGRADATION TYPES
   196	
   197	/** Fallback tier in the 3-tier degradation chain. */
   198	type FallbackTier = 1 | 2 | 3;
   199	
   200	/** Why degradation was triggered at a given tier. */
   201	interface DegradationTrigger {
   202	  reason: 'low_quality' | 'insufficient_results' | 'both';
   203	  topScore: number;
   204	  resultCount: number;
   205	  relativeGap?: number;
   206	}
   207	
   208	/** Record of a single degradation event during tiered fallback. */
   209	interface DegradationEvent {
   210	  tier: FallbackTier;
   211	  trigger: DegradationTrigger;
   212	  resultCountBefore: number;
   213	  resultCountAfter: number;
   214	}
   215	
   216	/**
   217	 * Absolute quality floor for degradation checks.
   218	 *
   219	 * Raw RRF scores are typically small decimals (often <0.05), so a
   220	 * high fixed threshold causes false degradations. Use a conservative floor and
   221	 * pair it with a relative-gap check to avoid score-scale coupling.
   222	 */
   223	const DEGRADATION_QUALITY_THRESHOLD = 0.02;
   224	
   225	/** Minimum relative separation between top-1 and top-2 scores. */
   226	const DEGRADATION_MIN_RELATIVE_GAP = 0.2;
   227	
   228	/** Minimum result count: must have >= this many results to stay at current tier. */
   229	const DEGRADATION_MIN_RESULTS = 3;
   230	
   231	// 5. MODULE STATE
   232	
   233	/** Default result limit when none is specified by the caller. */
   234	const DEFAULT_LIMIT = 20;
   235	/** Primary vector similarity floor for hybrid fallback passes (percentage units). */
   236	const PRIMARY_FALLBACK_MIN_SIMILARITY = 30;
   237	/** Secondary vector similarity floor for adaptive retry passes (percentage units). */
   238	const SECONDARY_FALLBACK_MIN_SIMILARITY = 17;
   239	/** Tier-2 vector similarity floor for quality-aware fallback (percentage units). */
   240	const TIERED_FALLBACK_MIN_SIMILARITY = 10;
   241	
   242	/** Minimum MMR candidates required for diversity reranking to be worthwhile. */
   243	const MMR_MIN_CANDIDATES = 2;
   244	
   245	/** Fallback lambda (diversity vs relevance) when intent is not in INTENT_LAMBDA_MAP. */
   246	const MMR_DEFAULT_LAMBDA = 0.7;
   247	
   248	/** Number of top results used as seeds for co-activation spreading. */
   249	const SPREAD_ACTIVATION_TOP_N = 5;
   250	
   251	/** Maximum contextual tree header length prepended to content (including brackets). */
   252	const CONTEXT_HEADER_MAX_CHARS = 100;
   253	/** Header/content separator characters added during contextual tree injection. */
   254	const CONTEXT_HEADER_SEPARATOR_CHARS = 1;
   255	/** Reserved token overhead per contextual header, calibrated to max header length. */
   256	const CONTEXT_HEADER_TOKEN_OVERHEAD = Math.ceil(
   257	  (CONTEXT_HEADER_MAX_CHARS + CONTEXT_HEADER_SEPARATOR_CHARS) / 4
   258	);
   259	
   260	let db: Database.Database | null = null;

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	---
     2	title: "Search Pipeline - 4-Stage Retrieval"
     3	description: "Four-stage retrieval pipeline: candidate generation, fusion, reranking and filtering."
     4	trigger_phrases:
     5	  - "search pipeline"
     6	  - "retrieval pipeline"
     7	  - "4-stage pipeline"
     8	  - "candidate generation"
     9	  - "fusion scoring"
    10	  - "reranking"
    11	  - "stage 4 filter"
    12	  - "score invariant"
    13	  - "MPAB chunk collapse"
    14	---
    15	
    16	# Search Pipeline - 4-Stage Retrieval
    17	
    18	A four-stage retrieval pipeline that takes a search query through candidate generation, score fusion, reranking and final filtering to produce ranked memory results.
    19	
    20	---
    21	
    22	## Table of Contents
    23	
    24	- [1. OVERVIEW](#1-overview)
    25	- [2. STRUCTURE](#2-structure)
    26	- [3. PIPELINE STAGES](#3-pipeline-stages)
    27	- [4. KEY INVARIANTS](#4-key-invariants)
    28	- [5. RELATED DOCUMENTS](#5-related-documents)
    29	
    30	---
    31	
    32	## 1. OVERVIEW
    33	
    34	The `pipeline/` directory implements the core retrieval pipeline behind `memory_search`. Each search request flows through four sequential stages, each with a defined I/O contract and clear responsibility boundary. The pipeline supports hybrid, vector and multi-concept search types with optional deep-mode query expansion, cross-encoder reranking, MMR diversity pruning and MPAB chunk-to-parent reassembly.
    35	
    36	Gate E alignment: pipeline ranking is not the source of continuity truth. Resume-oriented callers should anchor on `/spec_kit:resume` and the `handover.md -> _memory.continuity -> spec docs` chain before using pipeline-ranked evidence.
    37	
    38	The public API is a single function: `executePipeline(config)` exported from `index.ts`.
    39	
    40	---
    41	
    42	## 2. STRUCTURE
    43	
    44	| File | Description |
    45	|------|-------------|
    46	| `index.ts` | Public barrel export. Re-exports `executePipeline` from the orchestrator and all pipeline type definitions from `types.ts`. |
    47	| `orchestrator.ts` | Wires the four stages together in sequence. Passes each stage's output as input to the next and assembles the final `PipelineResult` with per-stage metadata. |
    48	| `stage1-candidate-gen.ts` | Stage 1: Candidate Generation. Runs search channels (hybrid, vector, multi-concept), applies deep-mode query expansion (R6), embedding-based expansion (R12), summary embeddings (R8), constitutional memory injection, quality threshold filtering and tier/contextType filtering. |
    49	| `stage2-fusion.ts` | Stage 2: Fusion + Signal Integration. The single authoritative scoring point. Applies 9 signal steps in fixed order: session boost, causal boost, co-activation spreading, community co-retrieval, graph signals, FSRS testing effect, intent weights (non-hybrid only, G2 prevention), artifact routing, feedback signals, artifact limiting, anchor metadata and validation metadata scoring. |
    50	| `stage3-rerank.ts` | Stage 3: Rerank + Aggregate. Applies cross-encoder reranking (remote or local GGUF), MMR diversity pruning and MPAB chunk collapse with parent document reassembly from the database. |
    51	| `stage4-filter.ts` | Stage 4: Filter + Annotate. Removes results below minimum memory state priority, enforces per-tier limits, runs TRM evidence-gap detection and attaches annotation metadata. Enforces the score immutability invariant at runtime. |
    52	| `types.ts` | All pipeline data contracts: `PipelineRow`, `Stage4ReadonlyRow`, `PipelineConfig`, stage I/O interfaces (`Stage1Input`/`Output` through `Stage4Input`/`Output`), `PipelineResult`, `ScoreSnapshot` and the `resolveEffectiveScore()` shared score resolution function. Also provides `captureScoreSnapshot()` and `verifyScoreInvariant()` for Stage 4 defence-in-depth. |
    53	
    54	---
    55	
    56	## 3. PIPELINE STAGES
    57	
    58	```text
    59	Query + Config
    60	      |
    61	      v
    62	  Stage 1: Candidate Generation
    63	      |  search channels, constitutional injection, quality filter
    64	      v
    65	  Stage 2: Fusion + Signal Integration
    66	      |  session/causal/co-activation boosts, intent weights,
    67	      |  artifact routing, feedback signals, FSRS write-back
    68	      v
    69	  Stage 3: Rerank + Aggregate
    70	      |  cross-encoder reranking, MMR diversity, MPAB chunk collapse
    71	      v
    72	  Stage 4: Filter + Annotate
    73	      |  state filter, per-tier limits, TRM evidence gap, annotations
    74	      v
    75	  PipelineResult { results, metadata, annotations, trace }
    76	```
    77	
    78	**Stage 1 - Candidate Generation** (`stage1-candidate-gen.ts`)
    79	- Runs one or more search channels based on `searchType` and `mode`.
    80	- Channels: hybrid (with optional deep-mode expansion), vector, multi-concept.
    81	- Optional R12 embedding expansion and R8 summary embedding channels.
    82	- Injects constitutional memories when absent and no tier filter is active.
    83	- Applies quality threshold and tier/contextType filters.
    84	
    85	**Stage 2 - Fusion + Signal Integration** (`stage2-fusion.ts`)
    86	- The only stage where scoring modifications happen (except Stage 3 reranking).
    87	- 9 signal steps applied in a fixed order that must not be reordered.
    88	- G2 prevention: intent weights are applied only for non-hybrid search types.
    89	- FSRS testing effect fires only when `trackAccess` is explicitly true.
    90	
    91	**Stage 3 - Rerank + Aggregate** (`stage3-rerank.ts`)
    92	- Cross-encoder reranking via remote API or local GGUF model.
    93	- MMR diversity pruning using per-intent lambda values.
    94	- MPAB chunk collapse: groups chunks by parent, elects best chunk, reassembles parent content from the database.
    95	- Preserves Stage 2 scores as `stage2Score` for auditability.
    96	
    97	**Stage 4 - Filter + Annotate** (`stage4-filter.ts`)
    98	- Memory state priority filtering, with the coldest retained-history rows treated as fallback evidence only.
    99	- Per-tier hard limits prevent any single tier from dominating results.
   100	- TRM evidence-gap detection (Z-score confidence check on score distribution).
   101	- Runtime score invariant verification via snapshot comparison.
   102	
   103	---
   104	
   105	## 4. KEY INVARIANTS
   106	
   107	1. **Single Scoring Point.** All score modifications happen in Stage 2 (fusion) or Stage 3 (reranking). Stage 4 must not change any score field.
   108	2. **G2 Double-Weighting Guard.** Intent weights are applied only for non-hybrid search types. Hybrid search incorporates intent weighting during RRF/RSF fusion internally.
   109	3. **Stage 4 Score Immutability.** Enforced at compile time via `Stage4ReadonlyRow` readonly fields and at runtime via `captureScoreSnapshot()` / `verifyScoreInvariant()`.
   110	4. **Score Resolution Consistency.** All stages use the shared `resolveEffectiveScore()` function from `types.ts` with fallback chain: `intentAdjustedScore` > `rrfScore` > `score` > `similarity/100`, clamped to [0, 1].
   111	
   112	---
   113	
   114	## 5. RELATED DOCUMENTS
   115	
   116	- `mcp_server/lib/search/` - Parent search directory containing hybrid search, vector index, cross-encoder and other search modules consumed by the pipeline.
   117	- `mcp_server/lib/ops/` - Background operations (file watcher, job queue) that feed data into the search index.
   118	- `@spec-kit/shared/contracts/retrieval-trace.ts` - Trace contract used for pipeline observability.
   119	- `@spec-kit/shared/algorithms/mmr-reranker.ts` - MMR algorithm used by Stage 3.

exec
/bin/zsh -lc "nl -ba .opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	"""MCP server for codebase indexing and querying.
     2	
     3	Supports two modes:
     4	1. Daemon-backed: ``create_mcp_server(client, project_root)`` — lightweight MCP
     5	   server that delegates to the daemon via a ``DaemonClient``.
     6	2. Legacy entry point: ``main()`` — backward-compatible ``cocoindex-code`` CLI that
     7	   auto-creates settings from env vars and delegates to the daemon.
     8	"""
     9	
    10	# Modified by spec-kit-skilled-agent-orchestration: 009 packet REQ-001..006 (see ../NOTICE)
    11	from __future__ import annotations
    12	
    13	import asyncio
    14	import json
    15	import os
    16	from pathlib import Path
    17	from typing import TYPE_CHECKING
    18	
    19	from mcp.server.fastmcp import FastMCP
    20	from pydantic import BaseModel, Field
    21	
    22	if TYPE_CHECKING:
    23	    from .client import DaemonClient
    24	
    25	from .protocol import IndexingProgress
    26	
    27	_MCP_INSTRUCTIONS = (
    28	    "Code search and codebase understanding tools."
    29	    "\n"
    30	    "Use when you need to find code, understand how something works,"
    31	    " locate implementations, or explore an unfamiliar codebase."
    32	    "\n"
    33	    "Provides semantic search that understands meaning --"
    34	    " unlike grep or text matching,"
    35	    " it finds relevant code even when exact keywords are unknown."
    36	)
    37	
    38	
    39	# === Pydantic Models for Tool Inputs/Outputs ===
    40	
    41	
    42	class CodeChunkResult(BaseModel):
    43	    """A single code chunk result."""
    44	
    45	    file_path: str = Field(description="Relative path to the file")
    46	    language: str = Field(description="Programming language")
    47	    content: str = Field(description="The code content")
    48	    start_line: int = Field(description="Starting line number (1-indexed)")
    49	    end_line: int = Field(description="Ending line number (1-indexed)")
    50	    score: float = Field(description="Similarity score (0-1, higher is better)")
    51	    raw_score: float = Field(description="Raw vector similarity score before reranking")
    52	    path_class: str = Field(description="Source path class used for bounded reranking")
    53	    rankingSignals: list[str] = Field(
    54	        default_factory=list,
    55	        description="Ranking boosts or penalties applied to this result",
    56	    )
    57	
    58	
    59	class SearchResultModel(BaseModel):
    60	    """Result from search tool."""
    61	
    62	    success: bool
    63	    results: list[CodeChunkResult] = Field(default_factory=list)
    64	    total_returned: int = Field(default=0)
    65	    offset: int = Field(default=0)
    66	    dedupedAliases: int = Field(default=0)
    67	    uniqueResultCount: int = Field(default=0)
    68	    message: str | None = None
    69	
    70	
    71	# === Daemon-backed MCP server factory ===
    72	
    73	
    74	def create_mcp_server(client: DaemonClient, project_root: str) -> FastMCP:
    75	    """Create a lightweight MCP server that delegates to the daemon."""
    76	    mcp = FastMCP("cocoindex-code", instructions=_MCP_INSTRUCTIONS)
    77	
    78	    @mcp.tool(
    79	        name="search",
    80	        description=(
    81	            "Semantic code search across the entire codebase"
    82	            " -- finds code by meaning, not just text matching."
    83	            " Use this instead of grep/glob when you need to find implementations,"
    84	            " understand how features work,"
    85	            " or locate related code without knowing exact names or keywords."
    86	            " Accepts natural language queries"
    87	            " (e.g., 'authentication logic', 'database connection handling')"
    88	            " or code snippets."
    89	            " Returns matching code chunks with file paths,"
    90	            " line numbers, and relevance scores."
    91	            " Start with a small limit (e.g., 5);"
    92	            " if most results look relevant, use offset to paginate for more."
    93	        ),
    94	    )
    95	    async def search(
    96	        query: str = Field(
    97	            description=(
    98	                "Natural language query or code snippet to search for."
    99	                " Examples: 'error handling middleware',"
   100	                " 'how are users authenticated',"
   101	                " 'database connection pool',"
   102	                " or paste a code snippet to find similar code."
   103	            )
   104	        ),
   105	        limit: int = Field(
   106	            default=5,
   107	            ge=1,
   108	            le=100,
   109	            description="Maximum number of results to return (1-100)",
   110	        ),
   111	        offset: int = Field(
   112	            default=0,
   113	            ge=0,
   114	            description="Number of results to skip for pagination",
   115	        ),
   116	        refresh_index: bool = Field(
   117	            default=True,
   118	            description=(
   119	                "Whether to incrementally update the index before searching."
   120	                " Set to False for faster consecutive queries"
   121	                " when the codebase hasn't changed."
   122	            ),
   123	        ),
   124	        languages: list[str] | None = Field(
   125	            default=None,
   126	            description="Filter by programming language(s). Example: ['python', 'typescript']",
   127	        ),
   128	        paths: list[str] | None = Field(
   129	            default=None,
   130	            description=(
   131	                "Filter by file path pattern(s) using GLOB wildcards (* and ?)."
   132	                " Example: ['src/utils/*', '*.py']"
   133	            ),
   134	        ),
   135	    ) -> SearchResultModel:
   136	        """Query the codebase index via the daemon."""
   137	        loop = asyncio.get_event_loop()
   138	        try:
   139	            if refresh_index:
   140	                await loop.run_in_executor(None, lambda: client.index(project_root))
   141	            resp = await loop.run_in_executor(
   142	                None,
   143	                lambda: client.search(
   144	                    project_root=project_root,
   145	                    query=query,
   146	                    languages=languages,
   147	                    paths=paths,
   148	                    limit=limit,
   149	                    offset=offset,
   150	                ),
   151	            )
   152	            return SearchResultModel(
   153	                success=resp.success,
   154	                results=[
   155	                    CodeChunkResult(
   156	                        file_path=r.file_path,
   157	                        language=r.language,
   158	                        content=r.content,
   159	                        start_line=r.start_line,
   160	                        end_line=r.end_line,
   161	                        score=r.score,
   162	                        raw_score=r.raw_score,
   163	                        path_class=r.path_class,
   164	                        rankingSignals=r.rankingSignals,
   165	                    )
   166	                    for r in resp.results
   167	                ],
   168	                total_returned=resp.total_returned,
   169	                offset=resp.offset,
   170	                dedupedAliases=resp.dedupedAliases,
   171	                uniqueResultCount=resp.uniqueResultCount,
   172	                message=resp.message,
   173	            )
   174	        except Exception as e:
   175	            return SearchResultModel(success=False, message=f"Query failed: {e!s}")
   176	
   177	    return mcp
   178	
   179	
   180	# Keep the old `mcp` global for backward compatibility in __init__.py
   181	mcp: FastMCP | None = None
   182	
   183	
   184	# === Backward-compatible entry point ===
   185	
   186	
   187	def _convert_embedding_model(env_model: str) -> tuple[str, str]:
   188	    """Convert old COCOINDEX_CODE_EMBEDDING_MODEL to (provider, model)."""
   189	    sbert_prefix = "sbert/"
   190	    if env_model.startswith(sbert_prefix):
   191	        return "sentence-transformers", env_model[len(sbert_prefix) :]
   192	    return "litellm", env_model
   193	
   194	
   195	def main() -> None:
   196	    """Backward-compatible entry point for ``cocoindex-code`` CLI.
   197	
   198	    Auto-detects/creates settings from env vars, then delegates to daemon.
   199	    """
   200	    import argparse
   201	
   202	    from .client import ensure_daemon
   203	    from .settings import (
   204	        EmbeddingSettings,
   205	        LanguageOverride,
   206	        default_project_settings,
   207	        default_user_settings,
   208	        find_legacy_project_root,
   209	        find_project_root,
   210	        project_settings_path,
   211	        save_project_settings,
   212	        save_user_settings,
   213	        user_settings_path,
   214	    )
   215	
   216	    parser = argparse.ArgumentParser(
   217	        prog="cocoindex-code",
   218	        description="MCP server for codebase indexing and querying.",
   219	    )
   220	    subparsers = parser.add_subparsers(dest="command")

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	// ────────────────────────────────────────────────────────────────
     2	// MODULE: Memory Context
     3	// ────────────────────────────────────────────────────────────────
     4	
     5	import { randomUUID } from 'crypto';
     6	import { readFileSync } from 'node:fs';
     7	
     8	// Layer definitions
     9	import * as layerDefs from '../lib/architecture/layer-definitions.js';
    10	import { checkDatabaseUpdated } from '../core/index.js';
    11	import { toErrorMessage } from '../utils/index.js';
    12	
    13	// Intent classifier
    14	import * as intentClassifier from '../lib/search/intent-classifier.js';
    15	import type { IntentTelemetry } from '../lib/search/intent-classifier.js';
    16	
    17	// Query-intent routing (Phase 020: structural/semantic/hybrid classification)
    18	import { classifyQueryIntent } from '../code_graph/lib/query-intent-classifier.js';
    19	import { buildContext } from '../code_graph/lib/code-graph-context.js';
    20	
    21	// Core handlers for routing
    22	import { handleMemorySearch } from './memory-search.js';
    23	import { handleMemoryMatchTriggers } from './memory-triggers.js';
    24	
    25	// Response envelope
    26	import { createMCPErrorResponse, createMCPResponse } from '../lib/response/envelope.js';
    27	
    28	// Token estimation
    29	import { estimateTokens } from '../formatters/token-metrics.js';
    30	import {
    31	  getPressureLevel,
    32	  type RuntimeContextStats,
    33	} from '../lib/cognitive/pressure-monitor.js';
    34	import * as workingMemory from '../lib/cognitive/working-memory.js';
    35	import * as sessionManager from '../lib/session/session-manager.js';
    36	
    37	// Telemetry
    38	import * as retrievalTelemetry from '../lib/telemetry/retrieval-telemetry.js';
    39	import { initConsumptionLog, logConsumptionEvent } from '../lib/telemetry/consumption-logger.js';
    40	import {
    41	  attachSessionTransitionTrace,
    42	  buildSessionTransitionTrace,
    43	  type SessionTransitionTrace,
    44	} from '../lib/search/session-transition.js';
    45	
    46	// Eval logger — fail-safe, no-op when SPECKIT_EVAL_LOGGING !== "true"
    47	import { logSearchQuery, logChannelResult, logFinalResult } from '../lib/eval/eval-logger.js';
    48	import * as vectorIndex from '../lib/search/vector-index.js';
    49	
    50	// Shared handler types
    51	import type { MCPResponse } from './types.js';
    52	
    53	// PI-B3: Folder discovery integration
    54	import { discoverSpecFolder, getSpecsBasePaths } from '../lib/search/folder-discovery.js';
    55	import {
    56	  isAutoResumeEnabled,
    57	  isFolderDiscoveryEnabled,
    58	  isPressurePolicyEnabled,
    59	  isIntentAutoProfileEnabled,
    60	} from '../lib/search/search-flags.js';
    61	import { buildResumeLadder, type ResumeLadderResult } from '../lib/resume/resume-ladder.js';
    62	
    63	// Feature catalog: Unified context retrieval (memory_context)
    64	// Feature catalog: Dual-scope memory auto-surface
    65	// Feature catalog: Provenance-rich response envelopes
    66	
    67	
    68	/* ───────────────────────────────────────────────────────────────
    69	   1. TYPES
    70	──────────────────────────────────────────────────────────────── */
    71	
    72	interface ContextMode {
    73	  readonly name: string;
    74	  readonly description: string;
    75	  readonly strategy: string;
    76	  readonly tokenBudget?: number;
    77	}
    78	
    79	interface ContextOptions {
    80	  specFolder?: string;
    81	  folderBoost?: { folder: string; factor: number };
    82	  tenantId?: string;
    83	  userId?: string;
    84	  agentId?: string;
    85	  limit?: number;
    86	  sessionId?: string;
    87	  enableDedup?: boolean;
    88	  includeContent?: boolean;
    89	  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
    90	  anchors?: string[];
    91	  profile?: string;
    92	  sessionTransition?: SessionTransitionTrace;
    93	}
    94	
    95	interface SessionLifecycleMetadata {
    96	  sessionScope: 'caller' | 'ephemeral';
    97	  requestedSessionId: string | null;
    98	  effectiveSessionId: string;
    99	  resumed: boolean;
   100	  eventCounterStart: number;
   101	  resumedContextCount: number;
   102	}
   103	
   104	interface ContextResult extends Record<string, unknown> {
   105	  strategy: string;
   106	  mode: string;
   107	}
   108	
   109	interface LayerInfo {
   110	  tokenBudget?: number;
   111	}
   112	
   113	interface ContextArgs {
   114	  input: string;
   115	  mode?: string;
   116	  intent?: string;
   117	  specFolder?: string;
   118	  tenantId?: string;
   119	  userId?: string;
   120	  agentId?: string;
   121	  limit?: number;
   122	  sessionId?: string;
   123	  enableDedup?: boolean;
   124	  includeContent?: boolean;
   125	  includeTrace?: boolean; // CHK-040: Forward to internal memory_search calls
   126	  tokenUsage?: number;
   127	  anchors?: string[];
   128	  /** REQ-D5-003: Presentation profile ('quick'|'research'|'resume'|'debug'). Default: full response. */
   129	  profile?: string;
   130	}
   131	
   132	/** T205: Token budget enforcement metadata */
   133	type DroppedAllResultsReason = 'impossible_budget' | 'parse_failed' | 'no_survivor_fits';
   134	
   135	interface TokenBudgetEnforcement {
   136	  budgetTokens: number;
   137	  preEnforcementTokens: number;
   138	  returnedTokens: number;
   139	  /** Backward-compatible alias of returnedTokens. */
   140	  actualTokens: number;
   141	  enforced: boolean;
   142	  truncated: boolean;
   143	  originalResultCount?: number;
   144	  returnedResultCount?: number;
   145	  droppedAllResultsReason?: DroppedAllResultsReason;
   146	}
   147	
   148	type PressureOverrideTargetMode = 'quick' | 'focused' | null;
   149	
   150	interface SessionLifecycleResolution {
   151	  requestedSessionId: string | null;
   152	  effectiveSessionId: string;
   153	  resumed: boolean;
   154	  priorMode: string | null;
   155	  counter: number;
   156	  error?: string;
   157	}
   158	
   159	interface EffectiveModeIntentClassification {
   160	  detectedIntent?: string;
   161	  intentConfidence: number;
   162	  intentEvidence: string[];
   163	  resumeHeuristicApplied: boolean;
   164	  source: 'explicit' | 'auto-detected';
   165	}
   166	
   167	interface EffectiveModeResolution {
   168	  effectiveMode: string;
   169	  pressureOverrideApplied: boolean;
   170	  pressureOverrideTargetMode: PressureOverrideTargetMode;
   171	  pressureWarning: string | null;
   172	  intentClassification: EffectiveModeIntentClassification;
   173	}
   174	
   175	interface BuildResponseMetaParams {
   176	  effectiveMode: string;
   177	  requestedMode: string;
   178	  tracedResult: ContextResult;
   179	  pressurePolicy: {
   180	    level: string;
   181	    ratio: number | null;
   182	    source: string;
   183	    warning: string | null;
   184	  };
   185	  pressureOverrideApplied: boolean;
   186	  pressureOverrideTargetMode: PressureOverrideTargetMode;
   187	  pressureWarning: string | null;
   188	  sessionLifecycle: SessionLifecycleMetadata;
   189	  effectiveBudget: number;
   190	  enforcement: TokenBudgetEnforcement;
   191	  intentClassification: EffectiveModeIntentClassification;
   192	  discoveredFolder?: string;
   193	  includeTrace: boolean;
   194	  sessionTransition: SessionTransitionTrace;
   195	  structuralRoutingNudge: StructuralRoutingNudgeMeta | null;
   196	  intentTelemetry: IntentTelemetry | null;
   197	}
   198	
   199	interface QueryIntentMetadata {
   200	  queryIntent: string;
   201	  routedBackend: string;
   202	  confidence: number;
   203	  matchedKeywords?: string[];
   204	}
   205	
   206	interface StrategyErrorPayload {
   207	  error: string;
   208	  code: string;
   209	  details: Record<string, unknown>;
   210	  hints: string[];
   211	  severity: string | null;
   212	}
   213	
   214	interface StructuralRoutingNudgeMeta {
   215	  advisory: true;
   216	  advisoryPreset: 'ready';
   217	  preferredTool: 'code_graph_query';
   218	  message: string;
   219	  preservesAuthority: 'session_bootstrap';
   220	}

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	// ───────────────────────────────────────────────────────────────
     2	// MODULE: Memory Triggers
     3	// ───────────────────────────────────────────────────────────────
     4	// Shared packages
     5	import { validateFilePath } from '@spec-kit/shared/utils/path-security';
     6	
     7	// Feature catalog: Trigger phrase matching (memory_match_triggers)
     8	// Feature catalog: BM25 trigger phrase re-index gate
     9	
    10	
    11	/* ───────────────────────────────────────────────────────────────
    12	   1. DEPENDENCIES
    13	──────────────────────────────────────────────────────────────── */
    14	
    15	// Core utilities
    16	import { ALLOWED_BASE_PATHS, checkDatabaseUpdated } from '../core/index.js';
    17	import { toErrorMessage } from '../utils/index.js';
    18	import { createFilePathValidator } from '../utils/validators.js';
    19	
    20	// Formatters
    21	import { calculateTokenMetrics, type TokenMetrics } from '../formatters/index.js';
    22	
    23	// Lib modules
    24	import * as triggerMatcher from '../lib/parsing/trigger-matcher.js';
    25	import * as workingMemory from '../lib/cognitive/working-memory.js';
    26	import * as attentionDecay from '../lib/cognitive/attention-decay.js';
    27	import * as tierClassifier from '../lib/cognitive/tier-classifier.js';
    28	import type { TierInput, StateStats } from '../lib/cognitive/tier-classifier.js';
    29	import * as coActivation from '../lib/cognitive/co-activation.js';
    30	
    31	// REQ-019: Standardized Response Structure
    32	import { createMCPSuccessResponse, createMCPEmptyResponse, createMCPErrorResponse } from '../lib/response/envelope.js';
    33	// T004: Consumption instrumentation
    34	import { initConsumptionLog, logConsumptionEvent } from '../lib/telemetry/consumption-logger.js';
    35	
    36	// Eval logger — fail-safe, no-op when SPECKIT_EVAL_LOGGING !== "true"
    37	import { logSearchQuery, logFinalResult } from '../lib/eval/eval-logger.js';
    38	
    39	// Shared handler types
    40	import type { MCPResponse } from './types.js';
    41	// C2 FIX: Import DB access for scope filtering
    42	import { initialize_db } from '../lib/search/vector-index-store.js';
    43	// T73: Import session manager for trusted session validation (IDOR prevention)
    44	import * as sessionManager from '../lib/session/session-manager.js';
    45	
    46	/* ───────────────────────────────────────────────────────────────
    47	   2. TYPES
    48	──────────────────────────────────────────────────────────────── */
    49	
    50	interface TriggerMatch {
    51	  memoryId: number;
    52	  specFolder: string;
    53	  filePath: string;
    54	  title: string | null;
    55	  matchedPhrases: string[];
    56	  importanceWeight: number;
    57	  [key: string]: unknown;
    58	}
    59	
    60	interface EnrichedTriggerMatch extends TriggerMatch {
    61	  attentionScore: number;
    62	  tier: string;
    63	  coActivated: boolean;
    64	}
    65	
    66	interface FormattedResult {
    67	  memoryId: number;
    68	  specFolder: string;
    69	  filePath: string;
    70	  title: string | null;
    71	  matchedPhrases: string[];
    72	  importanceWeight: number;
    73	  tier?: string;
    74	  attentionScore?: number;
    75	  content?: string;
    76	  coActivated?: boolean;
    77	  [key: string]: unknown;
    78	}
    79	
    80	interface DecayStats {
    81	  decayedCount: number;
    82	}
    83	
    84	interface CoActivatedMemory {
    85	  memoryId: number;
    86	}
    87	
    88	interface WorkingMemoryEntry {
    89	  memoryId: number;
    90	  attentionScore: number;
    91	}
    92	
    93	interface CognitiveStats {
    94	  enabled: boolean;
    95	  sessionId: string;
    96	  turnNumber: number;
    97	  decayApplied: number;
    98	  memoriesActivated: number;
    99	  coActivations: number;
   100	  tierDistribution: StateStats;
   101	  tokenMetrics: TokenMetrics;
   102	}
   103	
   104	interface TriggerArgs {
   105	  prompt: string;
   106	  specFolder?: string;
   107	  limit?: number;
   108	  session_id?: string;
   109	  turnNumber?: number;
   110	  include_cognitive?: boolean;
   111	  // C2 FIX: Scope fields to prevent cross-scope trigger leaks
   112	  tenantId?: string;
   113	  userId?: string;
   114	  agentId?: string;
   115	}
   116	
   117	/* ───────────────────────────────────────────────────────────────
   118	   2b. CONSTANTS
   119	──────────────────────────────────────────────────────────────── */
   120	
   121	/** Per-turn decay rate for attention scoring. */
   122	const TURN_DECAY_RATE = 0.98;
   123	const validateTieredFilePath = createFilePathValidator(ALLOWED_BASE_PATHS, validateFilePath);
   124	
   125	/* ───────────────────────────────────────────────────────────────
   126	   2c. HELPER FUNCTIONS
   127	──────────────────────────────────────────────────────────────── */
   128	
   129	/** Fetch full memory records required for FSRS tier classification. */
   130	function fetchMemoryRecords(memoryIds: number[]): Map<number, TierInput> {
   131	  const records = new Map<number, TierInput>();
   132	  if (memoryIds.length === 0) return records;
   133	
   134	  const db = attentionDecay.getDb();
   135	  if (!db) return records;
   136	
   137	  try {
   138	    const stmt = db.prepare(
   139	      'SELECT * FROM memory_index WHERE id = ?'
   140	    );
   141	    for (const id of memoryIds) {
   142	      const row = stmt.get(id) as TierInput | undefined;
   143	      if (row) {
   144	        records.set(row.id as number, row);
   145	      }
   146	    }
   147	  } catch (err: unknown) {
   148	    const message = toErrorMessage(err);
   149	    console.warn('[memory_match_triggers] Failed to fetch memory records:', message);
   150	  }
   151	
   152	  return records;
   153	}
   154	
   155	/** Get tiered content for a memory based on its tier state (HOT=full, WARM=summary, COLD=excluded) */
   156	async function getTieredContent(
   157	  memoryInfo: { filePath: string; title: string | null; triggerPhrases: string[] },
   158	  tier: string
   159	): Promise<string> {
   160	  if (tier === 'COLD' || tier === 'DORMANT' || tier === 'ARCHIVED') return '';
   161	  try {
   162	    const fs = await import('fs');
   163	    const validatedPath = validateTieredFilePath(memoryInfo.filePath);
   164	    const canonicalPath = validateTieredFilePath(fs.realpathSync(validatedPath));
   165	    const content = fs.readFileSync(canonicalPath, 'utf-8');
   166	    if (tier === 'HOT') return content;
   167	    // WARM tier returns truncated summary
   168	    return content.substring(0, 150) + (content.length > 150 ? '...' : '');
   169	  } catch (_error: unknown) {
   170	    console.warn('[memory-triggers] getTieredContent failed', {
   171	      filePath: memoryInfo.filePath, // server-side only; safe to log
   172	      tier,
   173	      error: _error instanceof Error ? _error.message : String(_error),
   174	    });
   175	    return '';
   176	  }
   177	}
   178	
   179	/* ───────────────────────────────────────────────────────────────
   180	   3. MATCH TRIGGERS HANDLER
   181	──────────────────────────────────────────────────────────────── */
   182	
   183	/** Handle memory_match_triggers tool - matches prompt against trigger phrases with cognitive decay */
   184	async function handleMemoryMatchTriggers(args: TriggerArgs): Promise<MCPResponse> {
   185	  const {
   186	    prompt,
   187	    limit: rawLimit = 3,
   188	    session_id: rawSessionId,
   189	    turnNumber: rawTurnNumber = 1,
   190	    include_cognitive: includeCognitive = true
   191	  } = args;
   192	
   193	  // Validate inputs before any I/O (checkDatabaseUpdated is deferred until after validation)
   194	  if (!prompt || typeof prompt !== 'string') {
   195	    return createMCPErrorResponse({
   196	      tool: 'memory_match_triggers',
   197	      error: 'prompt is required and must be a string',
   198	      code: 'E_VALIDATION',
   199	      details: { parameter: 'prompt' },
   200	      recovery: {
   201	        hint: 'Provide a non-empty string for the prompt parameter'
   202	      }
   203	    });
   204	  }
   205	
   206	  // T73 SECURITY: Validate caller-supplied sessionId through server-side session
   207	  // manager to prevent IDOR. Callers cannot read/write working memory for
   208	  // arbitrary sessions — only server-minted or previously tracked sessions.
   209	  let sessionId: string | undefined = rawSessionId;
   210	  if (rawSessionId) {
   211	    const trustedSession = sessionManager.resolveTrustedSession(rawSessionId, {
   212	      tenantId: args.tenantId,
   213	      userId: args.userId,
   214	      agentId: args.agentId,
   215	    });
   216	    if (trustedSession.error) {
   217	      console.warn(`[memory_match_triggers] SECURITY: Rejected untrusted sessionId "${rawSessionId}" — ${trustedSession.error}`);
   218	      return createMCPErrorResponse({
   219	        tool: 'memory_match_triggers',
   220	        error: trustedSession.error,

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	// ───────────────────────────────────────────────────────────────
     2	// MODULE: Code Graph Context Handler
     3	// ───────────────────────────────────────────────────────────────
     4	// MCP tool handler for code_graph_context — LLM-oriented graph neighborhoods.
     5	
     6	import { buildContext, type ContextArgs, type QueryMode } from '../lib/code-graph-context.js';
     7	import type { CodeGraphSeed } from '../lib/seed-resolver.js';
     8	import { ensureCodeGraphReady, type ReadyResult } from '../lib/ensure-ready.js';
     9	import * as graphDb from '../lib/code-graph-db.js';
    10	import { buildReadinessBlock } from '../lib/readiness-contract.js';
    11	
    12	export interface ContextHandlerArgs {
    13	  input?: string;
    14	  queryMode?: string;
    15	  subject?: string;
    16	  seeds?: Array<{
    17	    filePath?: string;
    18	    startLine?: number;
    19	    endLine?: number;
    20	    query?: string;
    21	    provider?: string;
    22	    source?: string;
    23	    file?: string;
    24	    range?: { start: number; end: number };
    25	    score?: number;
    26	    snippet?: string;
    27	    symbolName?: string;
    28	    kind?: string;
    29	    nodeId?: string;
    30	    symbolId?: string;
    31	  }>;
    32	  budgetTokens?: number;
    33	  profile?: string;
    34	  includeTrace?: boolean;
    35	}
    36	
    37	interface NormalizedSeedSource {
    38	  source?: string;
    39	  filePath: string;
    40	  startLine?: number;
    41	  endLine?: number;
    42	  symbolId?: string;
    43	  symbolName?: string;
    44	}
    45	
    46	type ContextReadiness = ReadyResult & { error?: string };
    47	
    48	function shouldBlockReadPath(readiness: ReadyResult): boolean {
    49	  return readiness.action === 'full_scan' && readiness.inlineIndexPerformed !== true;
    50	}
    51	
    52	function resolveDeadlineMs(profile: ContextArgs['profile']): number {
    53	  switch (profile) {
    54	    case 'quick':
    55	      return 250;
    56	    case 'debug':
    57	      return 700;
    58	    case 'research':
    59	      return 900;
    60	    default:
    61	      return 400;
    62	  }
    63	}
    64	
    65	function resolveSeedSource(args: ContextHandlerArgs, anchor: {
    66	  filePath: string;
    67	  startLine: number;
    68	  endLine: number;
    69	  symbolId: string | null;
    70	  fqName: string | null;
    71	}): string | undefined {
    72	  const normalizedSeeds: NormalizedSeedSource[] = (args.seeds ?? []).map((seed) => ({
    73	    source: typeof seed.source === 'string' && seed.source.trim().length > 0
    74	      ? seed.source
    75	      : seed.provider,
    76	    filePath: seed.provider === 'cocoindex'
    77	      ? (seed.file ?? seed.filePath ?? '')
    78	      : (seed.filePath ?? seed.file ?? ''),
    79	    startLine: seed.provider === 'cocoindex' ? seed.range?.start : seed.startLine,
    80	    endLine: seed.provider === 'cocoindex' ? seed.range?.end : seed.endLine,
    81	    symbolId: seed.symbolId,
    82	    symbolName: seed.symbolName,
    83	  }));
    84	
    85	  const match = normalizedSeeds.find((seed) => {
    86	    if (seed.symbolId && anchor.symbolId) {
    87	      return seed.symbolId === anchor.symbolId;
    88	    }
    89	    if (seed.symbolName && anchor.fqName) {
    90	      return seed.symbolName === anchor.fqName || anchor.fqName.endsWith(`.${seed.symbolName}`);
    91	    }
    92	    if (seed.filePath !== anchor.filePath) {
    93	      return false;
    94	    }
    95	    if (typeof seed.startLine === 'number' && seed.startLine !== anchor.startLine) {
    96	      return false;
    97	    }
    98	    if (typeof seed.endLine === 'number' && seed.endLine !== anchor.endLine) {
    99	      return false;
   100	    }
   101	    return true;
   102	  });
   103	
   104	  return match?.source;
   105	}
   106	
   107	/** Handle code_graph_context tool call */
   108	export async function handleCodeGraphContext(args: ContextHandlerArgs): Promise<{ content: Array<{ type: string; text: string }> }> {
   109	  let readiness: ContextReadiness = {
   110	    freshness: 'empty' as const,
   111	    action: 'none' as const,
   112	    inlineIndexPerformed: false,
   113	    reason: 'readiness check not run',
   114	  };
   115	
   116	  try {
   117	    // Auto-trigger: ensure graph is fresh before querying
   118	    try {
   119	      readiness = await ensureCodeGraphReady(process.cwd(), {
   120	        allowInlineIndex: true,
   121	        allowInlineFullScan: false,
   122	      });
   123	    } catch (err: unknown) {
   124	      // PR 4 / F71 step 5: surface as canonical 'error' freshness so
   125	      // buildReadinessBlock() maps it to canonicalReadiness='missing' +
   126	      // trustState='unavailable' automatically. Removes the manual
   127	      // trustState injection that previously lived at the response site.
   128	      readiness = {
   129	        freshness: 'error' as const,
   130	        action: 'none' as const,
   131	        inlineIndexPerformed: false,
   132	        reason: 'readiness_check_crashed',
   133	        error: err instanceof Error ? err.message : String(err),
   134	      };
   135	    }
   136	
   137	    if (shouldBlockReadPath(readiness)) {
   138	      const readinessBlock = buildReadinessBlock(readiness);
   139	      return {
   140	        content: [{
   141	          type: 'text',
   142	          text: JSON.stringify({
   143	            status: 'blocked',
   144	            message: `code_graph_full_scan_required: ${readiness.reason}`,
   145	            data: {
   146	              queryMode: args.queryMode ?? 'neighborhood',
   147	              blocked: true,
   148	              degraded: true,
   149	              graphAnswersOmitted: true,
   150	              requiredAction: 'code_graph_scan',
   151	              blockReason: 'full_scan_required',
   152	              readiness: readinessBlock,
   153	              canonicalReadiness: readinessBlock.canonicalReadiness,
   154	              trustState: readinessBlock.trustState,
   155	              lastPersistedAt: graphDb.getStats().lastScanTimestamp,
   156	            },
   157	          }, null, 2),
   158	        }],
   159	      };
   160	    }
   161	
   162	    const queryMode = (['neighborhood', 'outline', 'impact'].includes(args.queryMode ?? '')
   163	      ? args.queryMode as QueryMode
   164	      : 'neighborhood');
   165	
   166	    const seeds = (args.seeds ?? []).map((seed) => {
   167	      const source = typeof seed.source === 'string' && seed.source.trim().length > 0
   168	        ? seed.source
   169	        : seed.provider;
   170	      const cocoindexFile = seed.file ?? seed.filePath;
   171	
   172	      if (seed.provider === 'cocoindex' && cocoindexFile) {
   173	        return {
   174	          provider: 'cocoindex' as const,
   175	          file: cocoindexFile,
   176	          range: seed.range ?? { start: seed.startLine ?? 1, end: seed.endLine ?? seed.startLine ?? 1 },
   177	          score: seed.score ?? 0,
   178	          snippet: seed.snippet,
   179	          source,
   180	        };
   181	      }
   182	
   183	      if (seed.provider === 'manual' && seed.symbolName) {
   184	        return {
   185	          provider: 'manual' as const,
   186	          symbolName: seed.symbolName,
   187	          filePath: seed.filePath,
   188	          kind: seed.kind,
   189	          source,
   190	        };
   191	      }
   192	
   193	      if (seed.provider === 'graph' && seed.symbolId) {
   194	        return {
   195	          provider: 'graph' as const,
   196	          nodeId: seed.nodeId ?? seed.symbolId,
   197	          symbolId: seed.symbolId,
   198	          source,
   199	        };
   200	      }
   201	
   202	      return {
   203	        filePath: seed.filePath ?? seed.file ?? '',
   204	        startLine: seed.startLine ?? seed.range?.start,
   205	        endLine: seed.endLine ?? seed.range?.end,
   206	        query: seed.query,
   207	        source,
   208	      };
   209	    }) as unknown as CodeGraphSeed[];
   210	
   211	    const profile = (['quick', 'research', 'debug'].includes(args.profile ?? '') ? args.profile : undefined) as ContextArgs['profile'];
   212	    const deadlineMs = resolveDeadlineMs(profile);
   213	
   214	    const contextArgs: ContextArgs = {
   215	      input: args.input,
   216	      queryMode,
   217	      subject: args.subject,
   218	      seeds,
   219	      budgetTokens: args.budgetTokens ?? 1200,
   220	      deadlineMs,

exec
/bin/zsh -lc "nl -ba .opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/011-indexing-and-adaptive-fusion/spec.md | sed -n '1,180p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	---
     2	title: "Feature Specification: Indexing and Adaptive Fusion Enablement"
     3	template_source: "SPECKIT_TEMPLATE_SOURCE: spec-core | v2.2"
     4	description: "Feature Specification: Indexing and Adaptive Fusion Enablement"
     5	trigger_phrases:
     6	  - "indexing enablement"
     7	  - "adaptive fusion"
     8	  - "cocoindex path drift"
     9	importance_tier: "important"
    10	contextType: "implementation"
    11	---
    12	
    13	<!-- SPECKIT_TEMPLATE_SOURCE: spec-core | v2.2 -->
    14	<!-- SPECKIT_LEVEL: 2 -->
    15	<!-- CONTENT DISCIPLINE: PHASE PARENT
    16	  FORBIDDEN content (do NOT author at phase-parent level):
    17	    - merge/migration/consolidation narratives (consolidate*, merged from, renamed from, collapsed, X→Y, reorganization history)
    18	    - migrated from, ported from, originally in
    19	    - heavy docs: plan.md, tasks.md, checklist.md, decision-record.md, implementation-summary.md — these belong in child phase folders only
    20	  REQUIRED content (MUST author at phase-parent level):
    21	    - Root purpose: what problem does this entire phased decomposition solve?
    22	    - Sub-phase manifest: which child phase folders exist and what each one does
    23	    - What needs done: the high-level outcome the phases work toward
    24	-->
    25	
    26	# Feature Specification: Indexing and Adaptive Fusion Enablement
    27	
    28	<!-- ANCHOR:metadata -->
    29	## 1. METADATA
    30	
    31	| Field | Value |
    32	|-------|-------|
    33	| **Level** | 2 |
    34	| **Priority** | P0 |
    35	| **Status** | Review |
    36	| **Created** | 2026-03-31 |
    37	| **Branch** | `system-speckit/024-compact-code-graph` |
    38	| **Parent Spec** | `../spec.md` |
    39	| **Parent Packet** | `system-spec-kit/023-hybrid-rag-fusion-refinement` |
    40	| **Predecessor** | 010-search-retrieval-quality-fixes |
    41	| **Successor** | 012-memory-save-quality-pipeline |
    42	| **Handoff Criteria** | Validator + phase-parent trio stay current while child packets remain the detailed execution surface |
    43	<!-- /ANCHOR:metadata -->
    44	
    45	---
    46	
    47	<!-- ANCHOR:problem -->
    48	## 2. PROBLEM & PURPOSE
    49	
    50	### Problem Statement
    51	Feature Specification: Indexing and Adaptive Fusion Enablement
    52	
    53	### Purpose
    54	After repository path changes, indexing subsystems were inconsistent: CocoIndex environment paths were stale, code-graph initialization could fail lazily, and adaptive fusion defaults were not explicitly represented across MCP config surfaces. Lexical score visibility through fusion traces was also incomplete.
    55	
    56	> **Phase-parent note:** This spec.md is the ONLY authored document at the parent level. All detailed planning, task breakdowns, checklists, and decisions live in the child phase folders listed in the Phase Documentation Map below. This keeps the parent from drifting stale as phases execute and pivot.
    57	<!-- /ANCHOR:problem -->
    58	
    59	---
    60	
    61	<!-- ANCHOR:scope -->
    62	## 3. SCOPE
    63	
    64	### In Scope
    65	- Child packet `001-wire-promotion-gate/` remains the authoritative implementation surface for its phase.
    66	- Child packet `002-persist-tuned-thresholds/` remains the authoritative implementation surface for its phase.
    67	- Child packet `003-real-feedback-labels/` remains the authoritative implementation surface for its phase.
    68	- Child packet `004-fix-access-signal-path/` remains the authoritative implementation surface for its phase.
    69	- Maintain the parent-level phase manifest, navigation pointers, and status surface only.
    70	
    71	### Out of Scope
    72	- Rewriting child-phase plans, tasks, or checklists from this parent packet.
    73	- Using the parent spec as a changelog or migration-history ledger.
    74	- Treating parent heavy docs as the source of implementation truth.
    75	
    76	### Files to Change
    77	| File Path | Change Type | Phase | Description |
    78	|-----------|-------------|-------|-------------|
    79	| `.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/011-indexing-and-adaptive-fusion/spec.md` | Modify/Create | parent | Lean phase-parent specification and child manifest |
    80	| `.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/011-indexing-and-adaptive-fusion/description.json` | Modify | parent | Refresh save metadata for the migration pass |
    81	| `.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/011-indexing-and-adaptive-fusion/graph-metadata.json` | Modify | parent | Refresh derived child pointers and save timestamp |
    82	<!-- /ANCHOR:scope -->
    83	
    84	---
    85	
    86	<!-- ANCHOR:phase-map -->
    87	## PHASE DOCUMENTATION MAP
    88	
    89	> This spec uses phased decomposition. Each phase is an independently executable child spec folder. All implementation details (plan, tasks, checklist, decisions, continuity) live inside the phase children.
    90	
    91	| Phase | Folder | Focus | Status |
    92	|-------|--------|-------|--------|
    93	| 001 | `001-wire-promotion-gate/` | Wire Promotion Gate: Wire PromotionGate to Action | complete |
    94	| 002 | `002-persist-tuned-thresholds/` | Persist Tuned Thresholds: Phase 2 — Persist Tuned Thresholds | complete |
    95	| 003 | `003-real-feedback-labels/` | Real Feedback Labels: Real Feedback Labels for Evaluation | complete |
    96	| 004 | `004-fix-access-signal-path/` | Fix Access Signal Path | complete |
    97	| 005 | `005-e2e-integration-test/` | E2e Integration Test: Phase 5 — End-to-End Integration Test | complete |
    98	| 006 | `006-default-on-boost-rollout/` | Default On Boost Rollout: Default-ON Boost Rollout — Session, Causal & Deep Expansion | complete |
    99	| 007 | `007-external-graph-memory-research/` | External Graph Memory Research | complete |
   100	| 008 | `008-create-sh-phase-parent/` | Create Sh Phase Parent: Append Nested Child Phases in create.sh | complete |
   101	| 009 | `009-graph-retrieval-improvements/` | Graph Retrieval Improvements | complete |
   102	
   103	### Phase Transition Rules
   104	
   105	- Each phase MUST pass `validate.sh` independently before the next phase begins.
   106	- Parent spec tracks aggregate progress via this map.
   107	- Use `/spec_kit:resume system-spec-kit/023-hybrid-rag-fusion-refinement/011-indexing-and-adaptive-fusion/NNN-phase/` to resume a specific phase.
   108	- Run `validate.sh --recursive` on the parent to validate all phases as an integrated unit.
   109	
   110	### Phase Handoff Criteria
   111	
   112	| From | To | Criteria | Verification |
   113	|------|-----|----------|--------------|
   114	| 001 | 002 | 001-wire-promotion-gate is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `001-wire-promotion-gate/` |
   115	| 002 | 003 | 002-persist-tuned-thresholds is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `002-persist-tuned-thresholds/` |
   116	| 003 | 004 | 003-real-feedback-labels is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `003-real-feedback-labels/` |
   117	| 004 | 005 | 004-fix-access-signal-path is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `004-fix-access-signal-path/` |
   118	| 005 | 006 | 005-e2e-integration-test is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `005-e2e-integration-test/` |
   119	| 006 | 007 | 006-default-on-boost-rollout is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `006-default-on-boost-rollout/` |
   120	| 007 | 008 | 007-external-graph-memory-research is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `007-external-graph-memory-research/` |
   121	| 008 | 009 | 008-create-sh-phase-parent is validated and its child packet state is recorded. | `validate.sh --strict --no-recursive` on `008-create-sh-phase-parent/` |
   122	| 009 | Complete | Child packet validates and records implementation state. | `validate.sh --strict --no-recursive` on `009-graph-retrieval-improvements/` |
   123	<!-- /ANCHOR:phase-map -->
   124	
   125	---
   126	
   127	<!-- ANCHOR:questions -->
   128	## 4. OPEN QUESTIONS
   129	
   130	- Should any child packet status in the phase map be reclassified beyond the implementation-summary heuristic?
   131	- Does this parent packet need additional navigation references outside the lean trio for future resume flows?
   132	<!-- /ANCHOR:questions -->
   133	
   134	---
   135	
   136	## RELATED DOCUMENTS
   137	
   138	- **Phase children**: See sub-folders `[0-9][0-9][0-9]-*/` for per-phase `spec.md`, `plan.md`, and `tasks.md`.
   139	- **Parent packet metadata**: See `description.json` and `graph-metadata.json` for save lineage and active-child pointers.

exec
/bin/zsh -lc "nl -ba .opencode/commands/memory/search.md | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	---
     2	description: Unified continuity retrieval and analysis - canonical spec-doc context search, epistemic baselines, causal graph, ablation studies, and dashboards
     3	argument-hint: "<query> [--intent:<type>] | preflight <specFolder> <taskId> | postflight <specFolder> <taskId> | history <specFolder> | causal <memoryId> | link <sourceId> <targetId> <relation> | unlink <edgeId> | causal-stats | ablation | dashboard"
     4	allowed-tools: Read, spec_kit_memory_memory_context, spec_kit_memory_memory_quick_search, spec_kit_memory_memory_search, spec_kit_memory_memory_match_triggers, spec_kit_memory_task_preflight, spec_kit_memory_task_postflight, spec_kit_memory_memory_drift_why, spec_kit_memory_memory_causal_link, spec_kit_memory_memory_causal_stats, spec_kit_memory_memory_causal_unlink, spec_kit_memory_eval_run_ablation, spec_kit_memory_eval_reporting_dashboard, spec_kit_memory_memory_get_learning_history
     5	---
     6	
     7	# 🚨 MANDATORY FIRST ACTION - DO NOT SKIP
     8	
     9	**BEFORE READING ANYTHING ELSE IN THIS FILE, CHECK `$ARGUMENTS`:**
    10	
    11	```text
    12	IF $ARGUMENTS is empty, undefined, or contains only whitespace:
    13	    → STOP IMMEDIATELY
    14	    → Present the user with this question:
    15	        question: "What would you like to retrieve context for?"
    16	        options:
    17	          - label: "Add feature"
    18	            description: "Context for implementing a new feature"
    19	          - label: "Fix bug"
    20	            description: "Context for debugging and fixing an issue"
    21	          - label: "Refactor"
    22	            description: "Context for code restructuring"
    23	          - label: "Security audit"
    24	            description: "Context for security review"
    25	          - label: "Understand"
    26	            description: "Context for learning existing code"
    27	          - label: "Find spec"
    28	            description: "Context for spec document retrieval"
    29	          - label: "Find decision"
    30	            description: "Context for decision rationale lookup"
    31	          - label: "Analysis tools"
    32	            description: "Epistemic baselines, causal graph, ablation, dashboards"
    33	    → WAIT for user response
    34	    → If "Analysis tools" selected → Display ANALYSIS OVERVIEW (Section 8)
    35	    → Otherwise → Use their response to determine the intent and query
    36	    → Only THEN continue with this workflow
    37	
    38	IF $ARGUMENTS starts with a KNOWN ANALYSIS SUBCOMMAND (Section 3):
    39	    → Route to ANALYSIS MODE (Section 5)
    40	
    41	IF $ARGUMENTS contains a query (any other text):
    42	    → Route to RETRIEVAL MODE (Section 4)
    43	```
    44	
    45	**CRITICAL RULES:**
    46	- **DO NOT** infer query from conversation context
    47	- **DO NOT** assume the user's intent without explicit input
    48	- **DO NOT** proceed past this point without explicit query from user
    49	- The query and intent MUST come from `$ARGUMENTS` or user's answer above
    50	
    51	---
    52	
    53	# Memory Search Command
    54	
    55	Unified entry point for knowledge retrieval and analysis. Combines intent-aware context search (retrieval mode) with epistemic measurement, causal graph tools, and evaluation dashboards (analysis mode).
    56	
    57	---
    58	
    59	## 0. INSTRUCTIONS
    60	
    61	Start by classifying `$ARGUMENTS` into retrieval mode or analysis mode. Follow the routing contract below, prefer canonical packet sources in retrieval mode, and only invoke the analysis subcommands that match the user's explicit request.
    62	
    63	---
    64	
    65	```yaml
    66	role: Retrieval & Analysis Specialist
    67	purpose: Unified entry point combining intent-aware retrieval with epistemic measurement, causal graph, and evaluation tools
    68	action: Route through retrieval or analysis mode based on argument pattern
    69	
    70	operating_mode:
    71	  workflow: argument_routing
    72	  workflow_compliance: MANDATORY
    73	  approvals: none_required
    74	  tracking: intent_classification
    75	```
    76	
    77	---
    78	
    79	## 1. PURPOSE
    80	
    81	> **L1 Orchestration + L6 Analysis**: This command operates at both the L1 retrieval layer (orchestrating lower-level context-retrieval operations) and the L6 analysis layer (epistemic baselines, causal graph, evaluation). It provides a single entry point for all knowledge-related context-retrieval operations.
    82	
    83	Provide a unified entry point that:
    84	
    85	**Retrieval mode** (default):
    86	- Automatically detects task intent from the query
    87	- Applies task-specific weights for search optimization
    88	- Combines search + load in a single operation
    89	- Returns context with relevance explanation
    90	- Enforces L1 token budget constraints (target: ~2000 tokens per call)
    91	- Handles session deduplication for cross-session queries
    92	- Targets canonical packet sources first: `handover.md`, `_memory.continuity`, then the packet spec docs
    93	
    94	**Analysis mode** (subcommand-triggered):
    95	- Epistemic measurement: Capture knowledge baselines before and after tasks (`task_preflight`, `task_postflight`)
    96	- Causal graph: Trace decision lineage, create/remove causal links, view graph stats (`memory_drift_why`, `memory_causal_link`, `memory_causal_unlink`, `memory_causal_stats`)
    97	- Evaluation: Run channel ablation studies and view reporting dashboards (`eval_run_ablation`, `eval_reporting_dashboard`)
    98	- Learning history: View PREFLIGHT/POSTFLIGHT records and Learning Index trends (`memory_get_learning_history`)
    99	
   100	### Hybrid Retrieval Runtime (Retrieval Mode)
   101	
   102	The unified context tool runs a hybrid retrieval pipeline with **graph-first routing** (026):
   103	
   104	- **Graph channel has priority** in the fusion strategy: structural queries (callers, imports, dependencies) are routed to `code_graph_query` first, before semantic or lexical channels
   105	- Tri-channel retrieval (graph + vector/semantic + FTS5/BM25) with graph results given precedence in the fusion merge
   106	- CocoIndex semantic search (`mcp__cocoindex_code__search`) integrates as the vector/semantic channel, providing natural-language code discovery alongside indexed-continuity vector search
   107	- When graph and semantic channels miss or return weak results, a 3-tier FTS fallback activates: FTS5 full-text → BM25 keyword scoring → Grep/Glob filesystem search. Post-026 FTS5 remediation improved BM25 tokenization and ranking accuracy
   108	- Intent-adaptive fusion and reranking (weights adapt when `SPECKIT_ADAPTIVE_FUSION` is enabled, including the internal continuity profile: semantic `0.52`, keyword `0.18`, recency `0.07`, graph `0.23`)
   109	- MMR diversity pruning to reduce redundant chunks, with continuity-oriented Stage 3 passes using a dedicated lambda of `0.65`
   110	- Cross-encoder reranking only runs when at least 4 candidates reach Stage 3; `applyLengthPenalty` remains on the API surface for compatibility but currently resolves to a neutral `1.0` multiplier for every document
   111	- `getRerankerStatus()` exposes reranker latency plus cache `hits`, `misses`, `staleHits`, and `evictions`
   112	- Deep-mode query expansion for broader lexical coverage
   113	- Evidence-gap detection (026) to flag low-confidence retrievals with explicit gap warnings, enabling downstream reasoning to remain cautious and avoid acting on sparse evidence
   114	
   115	### Canonical Retrieval Order
   116	
   117	- `/spec_kit:resume` is the recovery surface for session continuation.
   118	- Resume-oriented retrieval follows `handover.md -> _memory.continuity -> spec docs`.
   119	- Packet-oriented retrieval may additionally use indexed `document_type='graph_metadata'` rows for dependency, supersession, related-packet, and key-file signals.
   120	- `find_spec` and `find_decision` should resolve against canonical spec docs and anchors, not against standalone continuity artifacts.
   121	
   122	---
   123	
   124	## 2. CONTRACT
   125	
   126	**Inputs:** `$ARGUMENTS`: Query with optional intent override, OR analysis subcommand with parameters
   127	**Outputs:** Context with relevance scores and intent explanation, OR `STATUS=<OK|FAIL>` with subcommand-specific output
   128	
   129	---
   130	
   131	## 3. QUICK REFERENCE
   132	
   133	### Retrieval Mode (default)
   134	
   135	| Command | Result |
   136	|---------|--------|
   137	| `/memory:search "implement auth"` | Auto-detect add_feature, apply weights |
   138	| `/memory:search "auth bug" --intent:fix_bug` | Explicit fix_bug intent |
   139	| `/memory:search "how does auth work?"` | Auto-detect understand intent |
   140	| `/memory:search "optimize auth code"` | Auto-detect refactor intent |
   141	| `/memory:search "auth security review"` | Auto-detect security_audit intent |
   142	| `/memory:search "find the spec for auth"` | Auto-detect find_spec intent |
   143	| `/memory:search "why did we choose JWT"` | Auto-detect find_decision intent |
   144	
   145	### Analysis Mode (subcommand-triggered)
   146	
   147	| Command | Result |
   148	|---------|--------|
   149	| `/memory:search preflight specs/007-auth T1` | Capture epistemic baseline |
   150	| `/memory:search postflight specs/007-auth T1` | Calculate learning delta |
   151	| `/memory:search history specs/007-auth` | View learning history |
   152	| `/memory:search causal 42` | Trace causal chain for memory #42 |
   153	| `/memory:search link 42 43 caused` | Link memory #42 → #43 as caused |
   154	| `/memory:search unlink 5` | Remove causal edge #5 |
   155	| `/memory:search causal-stats` | View causal graph statistics |
   156	| `/memory:search ablation` | Run channel ablation study |
   157	| `/memory:search dashboard` | View reporting dashboard |
   158	
   159	---
   160	
   161	## 4. ARGUMENT ROUTING
   162	
   163	```text
   164	$ARGUMENTS
   165	    │
   166	    ├─ Empty (no args)                        → INTERACTIVE PROMPT (see gate above)
   167	    │
   168	    ├─ ANALYSIS SUBCOMMAND DETECTED?
   169	    │   First token matches one of:
   170	    │   "preflight", "postflight", "history",
   171	    │   "causal", "link", "unlink",
   172	    │   "causal-stats", "ablation", "dashboard"
   173	    │   └─► YES → ANALYSIS MODE (Section 5)
   174	    │
   175	    └─ OTHERWISE (any other text)
   176	        └─► RETRIEVAL MODE (Section 4A)
   177	            Parse: <query> [--intent:<type>]
   178	```
   179	
   180	**Routing logic:** If the first argument token exactly matches a known analysis subcommand keyword → route to analysis mode. Otherwise → treat entire input as a retrieval query (with optional `--intent:` flag).
   181	
   182	---
   183	
   184	<!-- ═══════════════════════════════════════════════════════════════ -->
   185	<!-- SECTION 4A: RETRIEVAL MODE                                     -->
   186	<!-- ═══════════════════════════════════════════════════════════════ -->
   187	
   188	## 4A. RETRIEVAL MODE
   189	
   190	### Intent Types and Weights
   191	
   192	#### Intent Classification
   193	
   194	The system detects one of seven intent types:
   195	
   196	| Intent Type | Description | Weight Adjustments |
   197	|-------------|-------------|--------------------|
   198	| **add_feature** | Implementing new functionality | implementation: 1.5x, architecture: 1.3x, patterns: 1.2x |
   199	| **fix_bug** | Debugging and fixing issues | decisions: 1.4x, implementation: 1.3x, errors: 1.5x |
   200	| **refactor** | Code restructuring | architecture: 1.5x, patterns: 1.4x, decisions: 1.2x |
   201	| **security_audit** | Security review | decisions: 1.4x, implementation: 1.3x, security: 1.5x |
   202	| **understand** | Learning existing code | architecture: 1.4x, decisions: 1.3x, overview: 1.5x |
   203	| **find_spec** | Canonical spec document retrieval | spec-doc: 1.5x, architecture: 1.3x, overview: 1.2x |
   204	| **find_decision** | Decision rationale lookup from canonical docs | decisions: 1.5x, rationale: 1.4x, architecture: 1.2x |
   205	
   206	#### Detection Logic
   207	
   208	Intent is detected via keyword matching against the query. Keywords are phrase-based to avoid false positives:
   209	
   210	| Intent | Keywords |
   211	|--------|----------|
   212	| `add_feature` | 'implement', 'add feature', 'add new', 'add a', 'create new', 'build new' |
   213	| `fix_bug` | 'bug', 'error', 'fix', 'broken', 'issue', 'debug' |
   214	| `refactor` | 'refactor', 'restructure', 'improve', 'clean up', 'optimize' |
   215	| `security_audit` | 'security', 'vulnerability', 'auth', 'sanitize', 'xss', 'csrf' |
   216	| `understand` | 'how', 'why', 'what', 'explain', 'understand', 'learn' |
   217	| `find_spec` | 'spec', 'specification', 'spec folder', 'spec document', 'find spec' |
   218	| `find_decision` | 'decision', 'rationale', 'why did we', 'chose', 'decision record' |
   219	
   220	**Default fallback:** If no keywords match, defaults to `understand`.

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/orchestrator.ts | sed -n '1,180p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	// ───────────────────────────────────────────────────────────────
     2	// MODULE: Orchestrator
     3	// ───────────────────────────────────────────────────────────────
     4	// 4-stage pipeline execution with per-stage error handling and timeouts.
     5	//
     6	// B1 FIX: Each stage is wrapped in try/catch with withTimeout().
     7	// Stage 1 is mandatory (throws on failure — no candidates = no results).
     8	// Stages 2-4 fall back to previous stage output with degraded metadata.
     9	// Timing is recorded for latency observability.
    10	//
    11	// I/O CONTRACT:
    12	// Input:  PipelineConfig (query, embedding, limits, flags, intent, session)
    13	// Output: PipelineResult { results: Stage4ReadonlyRow[], metadata, annotations, trace }
    14	// Key invariants:
    15	//     - results are scored by Stage 2, reranked by Stage 3, filtered by Stage 4
    16	//     - Score fields are frozen after Stage 3; Stage 4 output scores == Stage 3 output scores
    17	//     - Stage metadata for all four stages is included for observability
    18	//     - When a stage degrades, metadata.degraded = true and timing tracks each stage
    19	// Side effects:
    20	//     - Delegates to each stage; see individual stage modules for their side effects
    21	
    22	import type {
    23	  PipelineConfig,
    24	  PipelineResult,
    25	  Stage1Output,
    26	  Stage2Output,
    27	  Stage3Output,
    28	  Stage4Output,
    29	  Stage4ReadonlyRow,
    30	  SignalStatus,
    31	} from './types.js';
    32	
    33	import { executeStage1 } from './stage1-candidate-gen.js';
    34	import { executeStage2 } from './stage2-fusion.js';
    35	import { executeStage3 } from './stage3-rerank.js';
    36	import { executeStage4 } from './stage4-filter.js';
    37	import { MemoryError, withTimeout } from '../../errors/core.js';
    38	
    39	// Feature catalog: 4-stage pipeline architecture
    40	// Feature catalog: 4-stage pipeline refactor
    41	
    42	
    43	/** Per-stage timeout in milliseconds. */
    44	const STAGE_TIMEOUT_MS = 10_000;
    45	
    46	/**
    47	 * Execute the 4-stage retrieval pipeline with per-stage error handling.
    48	 *
    49	 * Stage 1: Candidate Generation — MANDATORY (throws on failure)
    50	 * Stage 2: Fusion + Signal Integration — falls back to unsorted candidates
    51	 * Stage 3: Rerank + Aggregate — falls back to unranked scored results
    52	 * Stage 4: Filter + Annotate — falls back to unfiltered results
    53	 *
    54	 * @param config Pipeline configuration derived from search args
    55	 * @returns Pipeline result with stage metadata and timing
    56	 */
    57	export async function executePipeline(config: PipelineConfig): Promise<PipelineResult> {
    58	  const timing: Record<string, number> = {};
    59	  const pipelineStart = Date.now();
    60	  let degraded = false;
    61	
    62	  // -- Stage 1: Candidate Generation (MANDATORY — no fallback possible) --
    63	  let stage1Result: Stage1Output;
    64	  try {
    65	    const t0 = Date.now();
    66	    stage1Result = await withTimeout(
    67	      executeStage1({ config }),
    68	      STAGE_TIMEOUT_MS,
    69	      'Stage 1: Candidate Generation',
    70	    );
    71	    timing.stage1 = Date.now() - t0;
    72	  } catch (err) {
    73	    throw new MemoryError(
    74	      'PIPELINE_STAGE1_FAILED',
    75	      `Candidate generation failed: ${err instanceof Error ? err.message : String(err)}`,
    76	      { cause: err instanceof Error ? err.message : String(err) },
    77	    );
    78	  }
    79	
    80	  // -- Stage 2: Fusion + Signal Integration (falls back to unsorted candidates) --
    81	  let stage2Result: Stage2Output;
    82	  try {
    83	    const t0 = Date.now();
    84	    stage2Result = await withTimeout(
    85	      executeStage2({
    86	        candidates: stage1Result.candidates,
    87	        config,
    88	        stage1Metadata: stage1Result.metadata,
    89	      }),
    90	      STAGE_TIMEOUT_MS,
    91	      'Stage 2: Fusion',
    92	    );
    93	    timing.stage2 = Date.now() - t0;
    94	  } catch (err) {
    95	    const msg = err instanceof Error ? err.message : String(err);
    96	    console.warn(`[pipeline] Stage 2 failed, returning unscored candidates: ${msg}`);
    97	    degraded = true;
    98	    stage2Result = {
    99	      scored: stage1Result.candidates,
   100	      metadata: {
   101	        sessionBoostApplied: 'failed' as SignalStatus,
   102	        causalBoostApplied: 'failed' as SignalStatus,
   103	        intentWeightsApplied: 'failed' as SignalStatus,
   104	        artifactRoutingApplied: 'failed' as SignalStatus,
   105	        feedbackSignalsApplied: 'failed' as SignalStatus,
   106	        qualityFiltered: 0,
   107	        durationMs: 0,
   108	      },
   109	    };
   110	    timing.stage2 = 0;
   111	  }
   112	
   113	  // -- Stage 3: Rerank + Aggregate (falls back to unranked scored results) --
   114	  let stage3Result: Stage3Output;
   115	  try {
   116	    const t0 = Date.now();
   117	    stage3Result = await withTimeout(
   118	      executeStage3({
   119	        scored: stage2Result.scored,
   120	        config,
   121	      }),
   122	      STAGE_TIMEOUT_MS,
   123	      'Stage 3: Rerank',
   124	    );
   125	    timing.stage3 = Date.now() - t0;
   126	  } catch (err) {
   127	    const msg = err instanceof Error ? err.message : String(err);
   128	    console.warn(`[pipeline] Stage 3 failed, returning unranked results: ${msg}`);
   129	    degraded = true;
   130	    stage3Result = {
   131	      reranked: stage2Result.scored,
   132	      metadata: {
   133	        rerankApplied: false,
   134	        chunkReassemblyStats: {
   135	          collapsedChunkHits: 0,
   136	          chunkParents: 0,
   137	          reassembled: 0,
   138	          fallback: 0,
   139	        },
   140	        durationMs: 0,
   141	      },
   142	    };
   143	    timing.stage3 = 0;
   144	  }
   145	
   146	  // -- Stage 4: Filter + Annotate (falls back to unfiltered results) --
   147	  let stage4Result: Stage4Output;
   148	  try {
   149	    const t0 = Date.now();
   150	    stage4Result = await withTimeout(
   151	      executeStage4({
   152	        results: stage3Result.reranked as Stage4ReadonlyRow[],
   153	        config,
   154	        stage1Metadata: { constitutionalInjected: stage1Result.metadata.constitutionalInjected },
   155	      }),
   156	      STAGE_TIMEOUT_MS,
   157	      'Stage 4: Filter',
   158	    );
   159	    timing.stage4 = Date.now() - t0;
   160	  } catch (err) {
   161	    const msg = err instanceof Error ? err.message : String(err);
   162	    console.warn(`[pipeline] Stage 4 failed, returning unfiltered results: ${msg}`);
   163	    degraded = true;
   164	    stage4Result = {
   165	      final: stage3Result.reranked as Stage4ReadonlyRow[],
   166	      metadata: {
   167	        stateFiltered: 0,
   168	        constitutionalInjected: stage1Result.metadata.constitutionalInjected,
   169	        evidenceGapDetected: false,
   170	        durationMs: 0,
   171	      },
   172	      annotations: {
   173	        stateStats: {},
   174	        featureFlags: {},
   175	      },
   176	    };
   177	    timing.stage4 = 0;
   178	  }
   179	
   180	  timing.total = Date.now() - pipelineStart;

exec
/bin/zsh -lc "rg --files .opencode/specs/system-spec-kit | rg '(memory_search|memory-context|cocoindex|overfetch|hard-response|truncation|graph-and-context|compact-code-graph|hybrid-rag)'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/decision-record.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/spec.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/plan.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/checklist.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/tasks.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/description.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/implementation-summary.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/001-shared-payload-provenance-layer/graph-metadata.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/resource-map.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/decision-record.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/tasks.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/description.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/decision-record.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/spec.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/plan.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/checklist.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/tasks.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/description.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/implementation-summary.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/005-code-graph-auto-reindex-parity/graph-metadata.json
.opencode/specs/system-spec-kit/024-compact-code-graph/spec.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/decision-record.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/spec.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/plan.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/checklist.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/tasks.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/description.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/implementation-summary.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/031-copilot-startup-hook-wiring/graph-metadata.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/spec.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/plan.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/checklist.md
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/spec.md
.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/plan.md
.opencode/specs/system-spec-kit/024-compact-code-graph/034-workflow-split-and-token-insight-contracts/decision-record.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/004-cross-runtime-startup-surfacing-parity/decision-record.md
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.opencode/specs/system-spec-kit/024-compact-code-graph/012-cocoindex-ux-utilization/spec.md
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.opencode/specs/system-spec-kit/024-compact-code-graph/002-session-start-hook/review/deep-review-config.json
.opencode/specs/system-spec-kit/024-compact-code-graph/034-workflow-split-and-token-insight-contracts/tasks.md
.opencode/specs/system-spec-kit/024-compact-code-graph/034-workflow-split-and-token-insight-contracts/description.json
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.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/003-code-graph-operations-hardening/decision-record.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/003-code-graph-operations-hardening/spec.md
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.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/003-code-graph-operations-hardening/checklist.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/003-code-graph-operations-hardening/tasks.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/003-code-graph-operations-hardening/description.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/003-code-graph-operations-hardening/implementation-summary.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/003-code-graph-operations-hardening/graph-metadata.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/implementation-summary.md
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/graph-metadata.json
.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/research/deep-research-strategy.md
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/spec.md
.opencode/specs/system-spec-kit/024-compact-code-graph/024-hookless-priming-optimization/plan.md
.opencode/specs/system-spec-kit/024-compact-code-graph/031-normalized-analytics-reader/decision-record.md
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.opencode/specs/system-spec-kit/024-compact-code-graph/030-opencode-graph-plugin/prompt/claude-code-graph-runtime-retest.md
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     1	---
     2	title: CocoIndex Code Search Patterns
     3	description: Effective semantic search strategies for getting the best results from CocoIndex Code, including query writing, filters, and when to choose semantic search over Grep.
     4	trigger_phrases:
     5	  - search strategies
     6	  - write better queries
     7	  - semantic search tips
     8	  - cocoindex search patterns
     9	  - when to use semantic search
    10	---
    11	
    12	# CocoIndex Code Search Patterns
    13	
    14	Strategies for writing effective semantic queries and getting the best results from CocoIndex Code.
    15	
    16	---
    17	
    18	<!-- ANCHOR:overview -->
    19	## OVERVIEW
    20	
    21	Strategies and patterns for effective semantic code search using CocoIndex Code. Covers query writing, language and path filters, score interpretation, comparison with Grep, result verification workflows, and common query patterns by domain.
    22	
    23	---
    24	
    25	<!-- /ANCHOR:overview -->
    26	<!-- ANCHOR:writing-good-queries -->
    27	## 1. WRITING GOOD QUERIES
    28	
    29	Semantic search understands meaning, not just keywords. Write queries as you would describe what you are looking for to a colleague.
    30	
    31	### Recommended Query Ladder
    32	
    33	1. Start with a short concept phrase (3-5 words)
    34	2. Add a language filter when you know the language
    35	3. Add a path filter when you know the module
    36	4. Rephrase the concept only after filters are exhausted
    37	5. Switch to `Grep` for exact-text tasks
    38	
    39	### Use Natural Language
    40	
    41	| Good Query (semantic)                        | Bad Query (keyword-style)    |
    42	| -------------------------------------------- | ---------------------------- |
    43	| "how does user authentication work"          | "auth"                       |
    44	| "error handling in API route handlers"       | "try catch"                  |
    45	| "database connection pooling setup"          | "pool"                       |
    46	| "file upload processing and validation"      | "upload"                     |
    47	| "rate limiting middleware implementation"     | "rate limit"                 |
    48	
    49	### Be Specific About Intent
    50	
    51	The more specific your query, the better the results.
    52	
    53	| Vague (many irrelevant results)         | Specific (targeted results)                           |
    54	| --------------------------------------- | ----------------------------------------------------- |
    55	| "config"                                | "database configuration with connection parameters"   |
    56	| "test"                                  | "unit test setup with mock dependencies"              |
    57	| "error"                                 | "error recovery when external API calls fail"         |
    58	| "middleware"                            | "authentication middleware that validates JWT tokens"  |
    59	
    60	### Describe Intent, Not Syntax
    61	
    62	Semantic search finds code by what it does, not how it looks.
    63	
    64	```
    65	Instead of: "async function"
    66	Write:      "asynchronous request handlers"
    67	
    68	Instead of: "for loop array"
    69	Write:      "iterating over collection items"
    70	
    71	Instead of: "if err != nil"
    72	Write:      "error checking in Go functions"
    73	```
    74	
    75	---
    76	
    77	<!-- /ANCHOR:writing-good-queries -->
    78	<!-- ANCHOR:using-language-filters -->
    79	## 2. USING LANGUAGE FILTERS
    80	
    81	Filter by language when you know which language you need results from. CocoIndex Code supports **28+ languages** (see tool_reference.md for the full list).
    82	
    83	### When to Filter
    84	
    85	- You are working in a specific language and want only relevant results
    86	- The codebase has multiple implementations of the same concept in different languages
    87	- You want to avoid noise from documentation or config files
    88	
    89	### Examples
    90	
    91	The `--lang` flag is **repeatable** -- specify it multiple times to filter by multiple languages.
    92	
    93	```bash
    94	# Find Python database models
    95	ccc search "database model definitions" --lang python
    96	
    97	# Find TypeScript React components
    98	ccc search "form validation component" --lang tsx
    99	
   100	# Find Go error handling patterns
   101	ccc search "error handling and recovery" --lang go
   102	
   103	# Find SQL migration scripts
   104	ccc search "table creation with foreign keys" --lang sql
   105	
   106	# Filter by multiple languages at once
   107	ccc search "authentication middleware" --lang python --lang typescript
   108	
   109	# Three languages
   110	ccc search "data serialization" --lang python --lang rust --lang go
   111	```
   112	
   113	**MCP equivalent:** The MCP `search` tool uses `languages` (a list of strings) instead of `--lang`:
   114	```json
   115	{
   116	  "query": "authentication middleware",
   117	  "languages": ["python", "typescript"]
   118	}
   119	```
   120	
   121	### When NOT to Filter
   122	
   123	- You want to understand a concept across the whole codebase
   124	- You are exploring unfamiliar code and do not know what language to expect
   125	- You want to find documentation alongside implementation code
   126	
   127	---
   128	
   129	<!-- /ANCHOR:using-language-filters -->
   130	<!-- ANCHOR:using-path-filters -->
   131	## 3. USING PATH FILTERS
   132	
   133	Scope searches to specific directories when you know where to look.
   134	
   135	### Examples
   136	
   137	```bash
   138	# Search only in API handlers
   139	ccc search "request validation" --path src/api/
   140	
   141	# Search only in tests
   142	ccc search "mock database setup" --path tests/
   143	
   144	# Search in a specific module
   145	ccc search "user permissions" --path src/auth/
   146	
   147	# Combine with language filter (--lang is repeatable)
   148	ccc search "error handling" --path src/services/ --lang typescript
   149	ccc search "error handling" --path src/services/ --lang typescript --lang python
   150	```
   151	
   152	### When to Use Path Filters
   153	
   154	- You know the feature lives in a specific directory
   155	- You want to avoid matches from unrelated parts of the codebase
   156	- You are investigating a specific module or package
   157	- For cross-CLI consistency: prefer explicit path filters over relying on the current working directory
   158	
   159	---
   160	
   161	<!-- /ANCHOR:using-path-filters -->
   162	<!-- ANCHOR:combining-filters-for-precision -->
   163	## 4. COMBINING FILTERS FOR PRECISION
   164	
   165	Combine query specificity, language filters, and path filters for the most targeted results.
   166	
   167	```bash
   168	# Highly targeted: TypeScript error handling in API layer
   169	ccc search "error handling with retry logic" --lang typescript --path src/api/ --limit 5
   170	
   171	# Find Python tests for database operations
   172	ccc search "database integration test fixtures" --lang python --path tests/
   173	
   174	# Find Rust memory management in core library
   175	ccc search "memory allocation and deallocation" --lang rust --path src/core/
   176	
   177	# Multi-language search scoped to a directory
   178	ccc search "configuration loading" --lang python --lang typescript --path src/config/
   179	```
   180	
   181	---
   182	
   183	<!-- /ANCHOR:combining-filters-for-precision -->
   184	<!-- ANCHOR:interpreting-relevance-scores -->
   185	## 5. INTERPRETING RELEVANCE SCORES
   186	
   187	Each result includes a relevance score from 0.0 to 1.0.
   188	
   189	| Score Range | Meaning                                           | Action                      |
   190	| ----------- | ------------------------------------------------- | --------------------------- |
   191	| 0.8 - 1.0  | Strong match: very likely what you are looking for | Read this first             |
   192	| 0.6 - 0.8  | Good match: probably relevant                     | Worth reviewing             |
   193	| 0.4 - 0.6  | Moderate match: somewhat related                  | Scan for usefulness         |
   194	| 0.0 - 0.4  | Weak match: tangentially related at best          | Usually skip                |
   195	
   196	**Tips:**
   197	- If top results score below 0.5, try rephrasing your query
   198	- If all results score above 0.8, your query is well-targeted
   199	- Scores are relative to the query, not absolute quality measures
   200	

codex
Read-only pass. Memory MCP calls were cancelled, so this is from local `rg` plus direct file reads.

The search system is split into four main surfaces:

- **`memory_context`** is the L1 orchestration layer. It classifies query intent, can route toward code-graph context, and delegates to `memory_search` or `memory_match_triggers` as needed. See [memory-context.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:17).

- **`memory_search`** is the heavier indexed spec-memory search path. It now runs through a 4-stage pipeline: candidate generation, fusion, rerank/aggregate, then filter/annotate. Entry point: [memory-search.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:15). Pipeline overview: [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34).

- **`memory_match_triggers`** is the fast trigger-phrase path with cognitive/tier behavior: HOT gets full content, WARM gets summary, colder states are excluded. See [memory-triggers.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:183).

- **CocoIndex + code graph** handle code search. CocoIndex is semantic search by meaning, exposed as an MCP `search` tool in [server.py](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:78). Code graph handles structural lookups and compact neighborhoods; `code_graph_context` accepts CocoIndex seeds too. See [context.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts:107).

Spec/doc anchors worth knowing:

- `/memory:search` documents the intended runtime: graph-first for structural queries, tri-channel retrieval, CocoIndex semantic channel, FTS5/BM25 fallback, adaptive fusion, MMR, reranking, and evidence-gap warnings. See [search.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/commands/memory/search.md:100).
- The 4-stage retrieval contract is documented in [pipeline/README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:56).
- The major spec packet for indexing/adaptive fusion says the problem was stale CocoIndex paths, lazy code-graph init failures, and incomplete fusion trace visibility. See [spec.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/011-indexing-and-adaptive-fusion/spec.md:53).
- CocoIndex query guidance lives in [search_patterns.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/mcp-coco-index/references/search_patterns.md:31).

My read: this repo treats “search” as a layered retrieval stack, not one tool. Memory search is for spec/history continuity, CocoIndex is for semantic code discovery, code graph is for structural code questions, and `memory_context` is the router that tries to keep those lanes from collapsing into one another.
hook: Stop
hook: Stop Completed
2026-04-27T14:47:59.832239Z ERROR codex_core::session: failed to record rollout items: thread 019dcf68-5242-7542-a5b5-de95611e823a not found
tokens used
142,315
Read-only pass. Memory MCP calls were cancelled, so this is from local `rg` plus direct file reads.

The search system is split into four main surfaces:

- **`memory_context`** is the L1 orchestration layer. It classifies query intent, can route toward code-graph context, and delegates to `memory_search` or `memory_match_triggers` as needed. See [memory-context.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:17).

- **`memory_search`** is the heavier indexed spec-memory search path. It now runs through a 4-stage pipeline: candidate generation, fusion, rerank/aggregate, then filter/annotate. Entry point: [memory-search.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:15). Pipeline overview: [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:34).

- **`memory_match_triggers`** is the fast trigger-phrase path with cognitive/tier behavior: HOT gets full content, WARM gets summary, colder states are excluded. See [memory-triggers.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts:183).

- **CocoIndex + code graph** handle code search. CocoIndex is semantic search by meaning, exposed as an MCP `search` tool in [server.py](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/mcp-coco-index/mcp_server/cocoindex_code/server.py:78). Code graph handles structural lookups and compact neighborhoods; `code_graph_context` accepts CocoIndex seeds too. See [context.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts:107).

Spec/doc anchors worth knowing:

- `/memory:search` documents the intended runtime: graph-first for structural queries, tri-channel retrieval, CocoIndex semantic channel, FTS5/BM25 fallback, adaptive fusion, MMR, reranking, and evidence-gap warnings. See [search.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/commands/memory/search.md:100).
- The 4-stage retrieval contract is documented in [pipeline/README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/README.md:56).
- The major spec packet for indexing/adaptive fusion says the problem was stale CocoIndex paths, lazy code-graph init failures, and incomplete fusion trace visibility. See [spec.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/011-indexing-and-adaptive-fusion/spec.md:53).
- CocoIndex query guidance lives in [search_patterns.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/mcp-coco-index/references/search_patterns.md:31).

My read: this repo treats “search” as a layered retrieval stack, not one tool. Memory search is for spec/history continuity, CocoIndex is for semantic code discovery, code graph is for structural code questions, and `memory_context` is the router that tries to keep those lanes from collapsing into one another.
