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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: 019dcb07-18af-7bd1-a216-12b3619908be
--------
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 pull together the highest-signal references: likely code entry points plus any specs/docs that describe the search system. Since “search system” is a broad term here, I’ll anchor on files and symbols that actually use that wording or related search/index concepts.
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 direct repo reads. I’ll use exact search first, then pull the smallest set of files that look central.
exec
/bin/zsh -lc "rg --files . | rg '("'^|/)(specs|'"\\.opencode|code_graph|coco|memory|search|mcp_server|scripts)(/|"'$)|search|memory|coco|index'"'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
./.opencode/install_guides/MCP - Sequential Thinking.md
./.opencode/install_guides/SET-UP - Code Graph.md
./.opencode/install_guides/install_scripts/install-sequential-thinking.sh
./.opencode/install_guides/install_scripts/README.md
./.opencode/install_guides/install_scripts/_utils.sh
./.opencode/install_guides/install_scripts/install-all.sh
./.opencode/install_guides/SET-UP - Skill Advisor.md
./.opencode/install_guides/README.md
./.opencode/install_guides/SET-UP - Skill Creation.md
./.opencode/install_guides/SET-UP - Opencode Agents.md
./.opencode/install_guides/SET-UP - AGENTS.md
./.opencode/README.md
./.opencode/package-lock.json
./.opencode/commands/agent_router.md
./.opencode/plugins/spec-kit-skill-advisor.js
./.opencode/plugins/README.md
./.opencode/plugins/spec-kit-compact-code-graph.js
./.opencode/agents/improve-agent.md
./.opencode/agents/orchestrate.md
./.opencode/agents/review.md
./.opencode/agents/README.txt
./.opencode/agents/deep-research.md
./.opencode/agents/ultra-think.md
./.opencode/agents/write.md
./.opencode/agents/improve-prompt.md
./.opencode/agents/deep-review.md
./.opencode/agents/context.md
./.opencode/agents/debug.md
./.opencode/commands/create/assets/create_sk_skill_auto.yaml
./.opencode/commands/create/assets/create_changelog_auto.yaml
./.opencode/commands/create/assets/create_folder_readme_auto.yaml
./.opencode/commands/create/assets/create_testing_playbook_auto.yaml
./.opencode/commands/create/assets/create_agent_confirm.yaml
./.opencode/commands/create/assets/create_feature_catalog_confirm.yaml
./.opencode/commands/create/assets/create_sk_skill_confirm.yaml
./.opencode/commands/create/assets/create_agent_auto.yaml
./.opencode/commands/create/assets/create_feature_catalog_auto.yaml
./.opencode/commands/create/assets/create_testing_playbook_confirm.yaml
./.opencode/commands/create/assets/create_changelog_confirm.yaml
./.opencode/commands/create/assets/create_folder_readme_confirm.yaml
./.opencode/commands/create/folder_readme.md
./.opencode/commands/create/README.txt
./.opencode/commands/create/testing-playbook.md
./.opencode/commands/create/feature-catalog.md
./.opencode/commands/create/sk-skill.md
./.opencode/commands/create/changelog.md
./.opencode/commands/create/agent.md
./.opencode/commands/memory/README.txt
./.opencode/commands/memory/save.md
./.opencode/commands/memory/manage.md
./.opencode/commands/memory/learn.md
./.opencode/commands/memory/search.md
./.opencode/commands/spec_kit/assets/spec_kit_implement_auto.yaml
./.opencode/commands/spec_kit/assets/spec_kit_resume_auto.yaml
./.opencode/commands/spec_kit/assets/spec_kit_resume_confirm.yaml
./.opencode/commands/spec_kit/assets/spec_kit_deep-research_auto.yaml
./.opencode/commands/spec_kit/assets/spec_kit_deep-research_confirm.yaml
./.opencode/commands/spec_kit/assets/spec_kit_plan_auto.yaml
./.opencode/commands/spec_kit/assets/spec_kit_plan_confirm.yaml
./.opencode/commands/spec_kit/assets/spec_kit_deep-review_auto.yaml
./.opencode/commands/spec_kit/assets/spec_kit_complete_auto.yaml
./.opencode/commands/spec_kit/assets/spec_kit_implement_confirm.yaml
./.opencode/commands/spec_kit/assets/spec_kit_complete_confirm.yaml
./.opencode/commands/spec_kit/assets/spec_kit_deep-review_confirm.yaml
./.opencode/commands/spec_kit/README.txt
./.opencode/commands/spec_kit/plan.md
./.opencode/commands/spec_kit/deep-research.md
./.opencode/commands/spec_kit/resume.md
./.opencode/commands/spec_kit/deep-review.md
./.opencode/commands/spec_kit/implement.md
./.opencode/commands/spec_kit/complete.md
./.opencode/skills/cli-claude-code/README.md
./.opencode/commands/README.txt
./.opencode/skills/cli-claude-code/graph-metadata.json
./.opencode/skills/cli-claude-code/SKILL.md
./.opencode/skills/README.md
./.opencode/skills/mcp-chrome-devtools/SKILL.md
./.opencode/skills/cli-gemini/assets/prompt_templates.md
./.opencode/skills/cli-gemini/assets/prompt_quality_card.md
./.opencode/skills/cli-gemini/SKILL.md
./.opencode/skills/cli-claude-code/references/integration_patterns.md
./.opencode/skills/cli-claude-code/references/claude_tools.md
./.opencode/skills/cli-claude-code/references/agent_delegation.md
./.opencode/skills/cli-claude-code/references/cli_reference.md
./.opencode/commands/improve/assets/improve_improve-agent_confirm.yaml
./.opencode/commands/improve/assets/improve_improve-agent_auto.yaml
./.opencode/commands/improve/README.txt
./.opencode/commands/improve/prompt.md
./.opencode/commands/improve/agent.md
./.opencode/specs/descriptions.json
./.opencode/skills/mcp-chrome-devtools/scripts/install.sh
./.opencode/skills/cli-gemini/manual_testing_playbook/manual_testing_playbook.md
./.opencode/commands/doctor/assets/doctor_code-graph_apply.yaml
./.opencode/commands/doctor/assets/doctor_mcp_install.yaml
./.opencode/commands/doctor/assets/doctor_code-graph_confirm.yaml
./.opencode/commands/doctor/assets/doctor_skill-advisor_auto.yaml
./.opencode/commands/doctor/assets/doctor_skill-advisor_confirm.yaml
./.opencode/commands/doctor/assets/doctor_code-graph_auto.yaml
./.opencode/commands/doctor/assets/doctor_code-graph_apply-confirm.yaml
./.opencode/commands/doctor/assets/doctor_mcp_debug.yaml
./.opencode/commands/doctor/mcp_debug.md
./.opencode/skills/mcp-chrome-devtools/examples/multi-viewport-test.sh
./.opencode/skills/mcp-chrome-devtools/examples/README.md
./.opencode/skills/mcp-chrome-devtools/examples/animation-testing.sh
./.opencode/skills/mcp-chrome-devtools/examples/performance-baseline.sh
./.opencode/skills/mcp-chrome-devtools/INSTALL_GUIDE.md
./.opencode/skills/cli-gemini/manual_testing_playbook/07--prompt-templates/001-template-substitution.md
./.opencode/skills/cli-gemini/manual_testing_playbook/07--prompt-templates/002-clear-quality-card-application.md
./.opencode/skills/mcp-coco-index/assets/config_templates.md
./.opencode/skills/mcp-coco-index/SKILL.md
./.opencode/specs/skilled-agent-orchestration/037-cmd-merge-spec-kit-phase/spec.md
./.opencode/specs/skilled-agent-orchestration/037-cmd-merge-spec-kit-phase/plan.md
./.opencode/specs/skilled-agent-orchestration/037-cmd-merge-spec-kit-phase/checklist.md
./.opencode/specs/skilled-agent-orchestration/037-cmd-merge-spec-kit-phase/tasks.md
./.opencode/specs/skilled-agent-orchestration/037-cmd-merge-spec-kit-phase/description.json
./.opencode/specs/skilled-agent-orchestration/037-cmd-merge-spec-kit-phase/implementation-summary.md
./.opencode/specs/skilled-agent-orchestration/037-cmd-merge-spec-kit-phase/graph-metadata.json
./.opencode/commands/doctor/scripts/mcp-doctor.sh
./.opencode/commands/doctor/scripts/mcp-doctor-lib.sh
./.opencode/commands/doctor/skill-advisor.md
./.opencode/commands/doctor/mcp_install.md
./.opencode/commands/doctor/code-graph.md
./.opencode/skills/sk-improve-agent/assets/improvement_config.json
./.opencode/skills/sk-improve-agent/assets/improvement_charter.md
./.opencode/skills/sk-improve-agent/assets/improvement_config_reference.md
./.opencode/skills/sk-improve-agent/assets/improvement_strategy.md
./.opencode/skills/sk-improve-agent/assets/target_manifest.jsonc
./.opencode/skills/sk-improve-agent/SKILL.md
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/decision-record.md
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/spec.md
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/plan.md
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/checklist.md
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/tasks.md
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/description.json
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/implementation-summary.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/manual_testing_playbook.md
./.opencode/skills/cli-gemini/manual_testing_playbook/01--cli-invocation/003-explicit-model-selection.md
./.opencode/skills/cli-gemini/manual_testing_playbook/01--cli-invocation/002-json-output-mode.md
./.opencode/skills/cli-gemini/manual_testing_playbook/01--cli-invocation/001-direct-prompt-text-output.md
./.opencode/skills/mcp-coco-index/scripts/update.sh
./.opencode/skills/mcp-coco-index/scripts/doctor.sh
./.opencode/skills/mcp-coco-index/scripts/install.sh
./.opencode/skills/mcp-coco-index/scripts/ensure_ready.sh
./.opencode/skills/mcp-coco-index/scripts/common.sh
./.opencode/skills/mcp-coco-index/INSTALL_GUIDE.md
./.opencode/skills/mcp-code-mode/references/configuration.md
./.opencode/skills/mcp-code-mode/references/naming_convention.md
./.opencode/skills/mcp-code-mode/references/tool_catalog.md
./.opencode/skills/mcp-code-mode/references/architecture.md
./.opencode/skills/mcp-code-mode/references/workflows.md
./.opencode/skills/mcp-code-mode/graph-metadata.json
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/external_reference.md
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/spec.md
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/plan.md
./.opencode/skills/sk-improve-agent/scripts/score-candidate.cjs
./.opencode/skills/sk-improve-agent/scripts/mutation-coverage.cjs
./.opencode/skills/sk-improve-agent/scripts/reduce-state.cjs
./.opencode/skills/sk-improve-agent/scripts/promote-candidate.cjs
./.opencode/skills/sk-improve-agent/scripts/candidate-lineage.cjs
./.opencode/skills/sk-improve-agent/scripts/benchmark-stability.cjs
./.opencode/skills/sk-improve-agent/scripts/generate-profile.cjs
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/changelog/changelog-025-root.md
./.opencode/specs/system-spec-kit/025-nested-changelog-per-spec/graph-metadata.json
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/04--console-and-network/003-har-export.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/04--console-and-network/001-console-list.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/04--console-and-network/002-cookies-retrieval.md
./.opencode/skills/cli-gemini/manual_testing_playbook/04--agent-routing/004-write-and-ultra-think-roster-coverage.md
./.opencode/skills/cli-gemini/manual_testing_playbook/04--agent-routing/003-deep-research-agent-grounding.md
./.opencode/skills/cli-gemini/manual_testing_playbook/04--agent-routing/005-debug-agent-root-cause.md
./.opencode/skills/cli-gemini/manual_testing_playbook/04--agent-routing/002-review-agent-second-opinion.md
./.opencode/skills/cli-gemini/manual_testing_playbook/04--agent-routing/001-context-agent-exploration.md
./.opencode/skills/mcp-coco-index/manual_testing_playbook/manual_testing_playbook.md
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/scratch/test-results-dr028-030.md
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./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/scratch/test-results-dr024-027.md
./.opencode/skills/sk-improve-agent/scripts/tests/benchmark-stability.vitest.ts
./.opencode/skills/sk-improve-agent/scripts/tests/mutation-coverage.vitest.ts
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/tasks.md
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/description.json
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/implementation-summary.md
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/graph-metadata.json
./.opencode/skills/cli-gemini/manual_testing_playbook/03--built-in-tools/003-save-memory-persistence.md
./.opencode/skills/cli-gemini/manual_testing_playbook/03--built-in-tools/001-google-web-search-grounding.md
./.opencode/skills/cli-gemini/manual_testing_playbook/03--built-in-tools/004-file-reference-syntax.md
./.opencode/skills/cli-gemini/manual_testing_playbook/03--built-in-tools/002-codebase-investigator.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/06--recovery-and-failure/004-cleanup-leak.md
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./.opencode/skills/mcp-code-mode/mcp_server/index.ts
./.opencode/skills/mcp-code-mode/mcp_server/tsconfig.json
./.opencode/skills/mcp-code-mode/mcp_server/package-lock.json
./.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/004-root-path-env-var-override.md
./.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/003-status-verification.md
./.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/001-default-model-verification.md
./.opencode/skills/mcp-coco-index/manual_testing_playbook/03--configuration/002-project-settings-inspection.md
./.opencode/skills/cli-gemini/manual_testing_playbook/06--integration-patterns/002-json-output-processing-pipeline.md
./.opencode/skills/cli-gemini/manual_testing_playbook/06--integration-patterns/001-generate-review-fix-cycle.md
./.opencode/skills/cli-gemini/manual_testing_playbook/06--integration-patterns/003-background-execution-parallel.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/05--mcp-parallel-instances/003-close-and-select-page.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/05--mcp-parallel-instances/005-page-context-isolation.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/05--mcp-parallel-instances/002-dual-instance-parallel.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/05--mcp-parallel-instances/001-chrome-devtools-1-navigate.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/05--mcp-parallel-instances/004-multi-tab-same-instance.md
./.opencode/skills/mcp-code-mode/assets/env_template.md
./.opencode/skills/mcp-code-mode/assets/config_template.md
./.opencode/skills/mcp-code-mode/SKILL.md
./.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/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/improvement_config.json
./.opencode/skills/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/improvement-journal.jsonl
./.opencode/skills/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/candidate-lineage.json
./.opencode/skills/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/mutation-coverage.json
./.opencode/skills/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/trade-off-trajectory.json
./.opencode/skills/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/agent-improvement-state.jsonl
./.opencode/skills/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/README.md
./.opencode/skills/sk-improve-agent/scripts/tests/fixtures/low-sample-benchmark/benchmark-results.json
./.opencode/skills/sk-improve-agent/scripts/tests/candidate-lineage.vitest.ts
./.opencode/skills/sk-improve-agent/scripts/tests/trade-off-detector.vitest.ts
./.opencode/skills/sk-improve-agent/scripts/tests/improvement-journal.vitest.ts
./.opencode/skills/sk-improve-agent/scripts/run-benchmark.cjs
./.opencode/skills/sk-improve-agent/scripts/improvement-journal.cjs
./.opencode/skills/sk-improve-agent/scripts/rollback-candidate.cjs
./.opencode/skills/sk-improve-agent/scripts/trade-off-detector.cjs
./.opencode/skills/sk-improve-agent/scripts/scan-integration.cjs
./.opencode/skills/sk-improve-agent/scripts/check-mirror-drift.cjs
./.opencode/skills/cli-gemini/manual_testing_playbook/02--auto-approve-yolo/001-yolo-flag-sandboxed-write.md
./.opencode/skills/cli-gemini/manual_testing_playbook/02--auto-approve-yolo/002-approval-mode-comparison.md
./.opencode/skills/cli-gemini/README.md
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/research/deep-research-strategy.md
./.opencode/skills/mcp-code-mode/scripts/validate_config.py
./.opencode/skills/mcp-code-mode/scripts/update.sh
./.opencode/skills/mcp-code-mode/scripts/install.sh
./.opencode/skills/mcp-code-mode/INSTALL_GUIDE.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
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./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/02--protocol-discovery/003-search-cdp-method.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/02--protocol-discovery/001-list-cdp-domains.md
./.opencode/skills/mcp-chrome-devtools/manual_testing_playbook/02--protocol-discovery/002-describe-page-domain.md
./.opencode/skills/sk-improve-agent/manual_testing_playbook/manual_testing_playbook.md
./.opencode/skills/cli-gemini/references/integration_patterns.md
./.opencode/skills/cli-gemini/references/gemini_tools.md
./.opencode/skills/cli-gemini/references/agent_delegation.md
./.opencode/skills/cli-gemini/references/cli_reference.md
./.opencode/skills/cli-gemini/graph-metadata.json
./.opencode/skills/sk-code-full-stack/assets/mobile/swift/checklists/code_quality_checklist.md
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./.opencode/skills/mcp-coco-index/manual_testing_playbook/05--skill-advisor-integration/001-semantic-flag-routing.md
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./.opencode/skills/mcp-code-mode/manual_testing_playbook/manual_testing_playbook.md
./.opencode/specs/skilled-agent-orchestration/029-sk-deep-research-first-upgrade/research/iterations/iteration-010.md
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exec
/bin/zsh -lc "rg -n \"search system|memory_search|memory_context|memory_match_triggers|CocoIndex|cocoindex|search_index|vector|embedding|query expansion|rerank|BM25|semantic search\" . --glob '"'!node_modules/**'"' --glob '"'!**/.git/**'"'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 228ms:
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/001-search-fusion-tuning-prompts/deep-research-prompt.md:8:/spec_kit:deep-research:auto "Search fusion weight optimization and reranking threshold calibration for system-spec-kit MCP server" --max-iterations=15 --spec-folder=.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/001-search-fusion-tuning-prompts/deep-research-prompt.md:13:**Topic:** Investigate whether the hardcoded thresholds, weights, and decay constants in the spec-kit search pipeline (cross-encoder reranking, stage2 fusion, vector-index decay) are optimal for spec-doc retrieval.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/001-search-fusion-tuning-prompts/deep-research-prompt.md:21:- `.opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts` - reranking models, thresholds, cache, circuit breaker
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/001-search-fusion-tuning-prompts/deep-research-prompt.md:23:- `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts` - embedding dim, FSRS decay, search weights config
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/001-search-fusion-tuning-prompts/deep-research-prompt.md:30:3. What is the latency distribution across reranking providers (Voyage/Cohere/Local)?
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-4-prompt.md:48:`--cd` is set here. **Permission:** read any of the 5 phase folders + their `external/` subfolders for evidence. You may also read **Public's own retrieval-stack code** (CocoIndex, Code Graph MCP, Spec Kit Memory) for the Public baseline column — see §"Public baseline" below.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-4-prompt.md:61:4. **Semantic query** — Can you ask "find code that does X" via embeddings / NL search / concept retrieval?
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-4-prompt.md:80:- **CocoIndex** for semantic query — read `.opencode/skills/mcp-coco-index/SKILL.md` and `.opencode/skills/mcp-coco-index/scripts/` if needed
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/deep-research-strategy.md:138:- Case F (100+ files): no FILES cap, oversized memories with diluted embeddings and placeholder descriptions
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:71:    "prompt": "Check SHA-256 dedup (TM-02) on re-save. Capture the evidence needed to prove Second save returns skip/no-op status; no new embedding row created; content hash matches; and the save-path/content-hash queries use exact-match scope clauses rather than nullable OR predicates. Return a concise user-facing pass/fail verdict with the main reason.",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:74:      "no new embedding row created",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:81:      "no new embedding row created",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:87:      "Command sequence is not expressible as direct handler calls: 1) Save once 2) Save identical payload 3) Verify embedding skipped 4) Capture SQL-shape evidence for the unchanged-save and content-hash probes"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:221:    "prompt": "\"Re-chunk a parent memory and verify safe-swap finalization stays atomic.\" Capture the evidence needed to prove New chunks index in staged state before old deletion; finalization moves parent attach + old-child unlink/delete into one transaction; failed finalization cleans the staged chunk tree; all-chunks-failed rollback preserves old children and the old parent BM25 state. Return a concise user-facing pass/fail verdict with the main reason.",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:226:      "all-chunks-failed rollback preserves old parent BM25 state",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:234:      "all-chunks-failed rollback preserves old parent BM25 state",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/08--bug-fixes-and-data-integrity.json:325:      "Command sequence is not expressible as direct handler calls: 1) Set invalid VOYAGE_API_KEY or OPENAI_API_KEY 2) Call memory_search to trigger provider error 3) Inspect response.summary, response.data.error, response.data.details"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-13-prompt.md:32:| `.opencode/skills/mcp-coco-index/` | CocoIndex semantic search |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/15--retrieval-enhancements.json:268:        "name": "memory_search",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/15--retrieval-enhancements.json:282:        "step": "memory_search({ query:\"spec folder context headers\", includeContent:true, includeTrace:true, limit:5 })",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/15--retrieval-enhancements.json:285:          "name": "memory_search",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/gate-i-execution-report/15--retrieval-enhancements.json:307:          "{\"summary\":\"> **[EVIDENCE GAP DETECTED]: Retrieved context has low mathematical confidence (Z=1.41). Consider first principles.**\\n\\nNo matching memories found\",\"data\":{\"count\":0,\"searchType\":\"hybrid\",\"constitutionalCount\":0,\"requestQuality\":{\"label\":\"gap\"},\"stateStats\":{\"minState\":\"\",\"before\":{\"UNKNOWN\":5},\"after\":{\"UNKNOWN\":5},\"removed\":0},\"featureFlags\":{\"trmEnabled\":true,\"multiQueryEnabled\":true,\"stateLimitsApplied\":false},\"pipelineMetadata\":{\"stage1\":{\"searchType\":\"hybrid\",\"channelCount\":2,\"activeChannels\":2,\"candidateCount\":5,\"constitutionalInjected\":0,\"durationMs\":18},\"stage2\":{\"sessionBoostApplied\":\"off\",\"causalBoostApplied\":\"applied\",\"intentWeightsApplied\":\"off\",\"artifactRoutingApplied\":\"applied\",\"feedbackSignalsApplied\":\"off\",\"graphContribution\":{\"killSwitchActive\":false,\"causalBoosted\":1,\"coActivationBoosted\":0,\"communityInjected\":0,\"graphSignalsBoosted\":0,\"totalGraphInjected\":0,\"rolloutState\":\"bounded_runtime\"},\"qualityFiltered\":0,\"durationMs\":1,\"recencyFusionApplied\":true,\"recencyFusionBoosted\":3,\"coActivationApplied\":true,\"graphSignalsApplied\":true},\"stage3\":{\"rerankApplied\":true,\"rerankProvider\":\"fallback-sort\",\"chunkReassemblyStats\":{\"collapsedChunkHits\":0,\"chunkParents\":0,\"reassembled\":0,\"fallback\":0},\"durationMs\":0},\"stage4\":{\"stateFiltered\":0,\"constitutionalInjected\":0,\"evidenceGapDetected\":true,\"durationMs\":0},\"timing\":{\"stage1\":18,\"stage2\":1,\"stage3\":0,\"stage4\":0,\"total\":19}},\"lexicalPath\":\"fts5\",\"fallbackState\":\"ok\",\"evidenceGapWarning\":\"> **[EVIDENCE GAP DETECTED]: Retrieved context has low mathematical confidence (Z=1.41). Consider first principles.**\",\"intent\":{\"type\":\"understand\",\"confidence\":1,\"description\":\"Understanding or exploring the codebase\",\"weightsApplied\":\"off\"},\"artifactRouting\":{\"strategy\":{\"artifactClass\":\"spec\",\"semanticWeight\":0.7,\"keywordWeight\":0.3,\"recencyBias\":0.2,\"maxResults\":5,\"boostFactor\":1},\"detectedClass\":\"spec\",\"confidence\":0.16666666666666666},\"artifact_routing\":{\"strategy\":{\"artifactClass\":\"spec\",\"semanticWeight"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-45__modular-architecture.md:1223:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "004-speckit/012-path-scoped-rules/002-modular-architecture" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-45__modular-architecture.md:1228:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-45__modular-architecture.md:1354:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-45__modular-architecture.md:1355:embedding_version: "1.0"
./.opencode/changelog/agents-md/v2.2.0.0.md:7:People needed clearer support for this new part of the workflow. (P1). FS-Enterprises "Resume prior work" row: added /memory:continue and memory_search() alternative (was missing, present in Universal + Barter). This makes the workflow easier to discover and use.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/012-command-alignment/scratch/archive-2026-03-25/iteration-001.md:27:### [F-002] [P1] `/memory:manage` includes `memory_search`, breaking 15-tool ownership contract
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/012-command-alignment/scratch/archive-2026-03-25/iteration-001.md:29:- **Evidence**: `allowed-tools` includes `spec_kit_memory_memory_search` (`manage.md:4`) and Appendix signatures include `spec_kit_memory_memory_search({...})` (`manage.md:866`), but canonical matrix assigns `memory_search` to `/memory:analyze` (`README.txt:255`) and states `/memory:manage` owns 15 tools (`README.txt:293`).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/012-command-alignment/scratch/archive-2026-03-25/iteration-001.md:31:- **Fix**: Remove `memory_search` from `/memory:manage` allowed/signature docs, or update README mapping/counts if ownership is intentionally expanded.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/012-command-alignment/scratch/archive-2026-03-25/iteration-001.md:38:  - Downgrade Trigger: If docs explicitly classify `memory_search` as helper-only and keep ownership counts primary-only.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/012-command-alignment/scratch/archive-2026-03-25/iteration-001.md:68:- **Evidence**: Quick search is "Option 2" (`analyze.md:796`), manual `memory_search` is "Option 3" (`analyze.md:807`), but text says manual search is "Option 2" (`analyze.md:874`).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/scratch/shared-memory-audit.md:80:1. If shared retrieval parity matters for trigger mode, teach `memory_match_triggers` to resolve `allowedSharedSpaceIds`.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-27__modular-architecture.md:241:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "004-speckit/012-path-scoped-rules/002-modular-architecture" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-27__modular-architecture.md:246:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-27__modular-architecture.md:362:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-27__modular-architecture.md:363:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/plan.md:116:# This tests embeddings, sqlite, vector operations
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-36__modular-architecture.md:466:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "004-speckit/012-path-scoped-rules/002-modular-architecture" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-36__modular-architecture.md:471:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-36__modular-architecture.md:600:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_15-36__modular-architecture.md:601:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/checklist.md:57:  - Server initializes, loads embeddings model
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-014.md:127:**Problem:** There is NO cap. If `effectiveFiles` has 300 entries (common for large sessions with enrichment from git context and spec-folder scanning), all 300 become `KEY_FILES` in the template. This bloats the rendered memory file and wastes embedding tokens.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_14-51__modular-architecture.md:293:- Indexed as memory #131 with semantic embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_14-51__modular-architecture.md:1585:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "004-speckit/012-path-scoped-rules/002-modular-architecture" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_14-51__modular-architecture.md:1590:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_14-51__modular-architecture.md:1716:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/023-path-scoped-rules/002-modular-architecture/scratch/legacy-memory-quarantine/24-12-25_14-51__modular-architecture.md:1717:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:400:### OBSERVATION: Tool: semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:402:Executed semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:404:**Details:** Tool: semantic_memory_memory_match_triggers | Status: completed
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:518:Check embeddings.js imports
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:526:Find require statements in embeddings.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:534:Find HuggingFace import in embeddings.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:979:**Tool: semantic_memory_memory_match_triggers**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:980:Tool: semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1015:**Tool: semantic_memory_memory_match_triggers**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1016:Tool: semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1051:**Tool: semantic_memory_memory_match_triggers**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1052:Tool: semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1087:**Tool: semantic_memory_memory_match_triggers**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1088:Tool: semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1129:**Tool: semantic_memory_memory_match_triggers**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1130:Tool: semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1165:**Tool: semantic_memory_memory_match_triggers**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1166:Tool: semantic_memory_memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1291:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/039-node-modules-consolidation" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1296:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1431:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/039-node-modules-consolidation/scratch/legacy-memory-quarantine/25-12-25_18-55__node-modules-consolidation.md:1432:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/012-command-alignment/scratch/archive-2026-03-25/iteration-007.md:34:- **Evidence**: Shows Schema v13; actual SCHEMA_VERSION = 23 in vector-index-schema.ts:143.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-6-prompt.md:65:- **CocoIndex** (semantic query)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-6-prompt.md:74:| **med** | Candidate requires modifying ONE surface or adding a small adapter, but doesn't conflict with the other two. Example: a new index type added to CocoIndex. |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-6-prompt.md:84:- **Which Public surface(s) it touches** (CocoIndex / Code Graph / Spec Kit Memory / new surface)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-6-prompt.md:138:- **CocoIndex** = semantic query (vector embeddings)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/scratch/iteration-6-prompt.md:150:| 1 | … | 002 | source-portable | CocoIndex | low | … |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/012-query-intelligence/scratch/reaudit-2026-03-23/codex53-verifier.md:46:Function verification: `expandQueryWithEmbeddings()` at [embedding-expansion.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:181), `isExpansionActive()` at :300, `expandQuery()` at [query-expander.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/query-expander.ts:73).  
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/012-query-intelligence/scratch/reaudit-2026-03-23/codex53-verifier.md:48:Behavior: stop-words + min token length 3 enforced at [embedding-expansion.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts:72), :75, :135-:137; simple-query suppression at :196-:199; Stage1 baseline+expanded parallel run and baseline-first dedup at [stage1-candidate-gen.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:552)-:577.  
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/012-query-intelligence/scratch/reaudit-2026-03-23/codex53-verifier.md:61:File verification: all 7 catalog-listed refs exist (catalog refs at [08-hyde-hypothetical-document-embeddings.md](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/feature_catalog/12--query-intelligence/08-hyde-hypothetical-document-embeddings.md:36)-:40, :46, :54).  
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:140:Completed full documentation alignment across 6 files to match the actual semantic memory MCP server v12.0.0 implementation. All documentation now reflects the correct tool definitions, tier values, embedding dimensions, and features.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:157:- Updated memory_search parameters to include tier, contextType, useDecay, includeContiguity, includeConstitutional
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:166:- Fixed embedding dimensions: 384 → 768 (nomic-embed-text-v1.5)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:169:- Updated embedding model config to show actual dimensions
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:225:1. **memory_search** - Semantic vector search with hybrid FTS5 fusion
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:227:3. **memory_match_triggers** - Fast trigger phrase matching (<50ms)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:319:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "specs/005-memory/004-auto-indexing" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:324:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:440:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-39__docs-alignment-v12.md:441:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-012.md:369:  "sessionSummary": "Designed and implemented the hybrid RAG fusion pipeline with BM25, vector, and graph channels. Calibrated RRF K parameter to 55 based on ablation study results. Added ground truth queries for 15 memory entries.",
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-012.md:376:    { "userInput": "Run the ablation study on all channels", "assistantResponse": "Executed ablation across vector, BM25, FTS5, graph, and trigger channels. Results show vector+BM25 achieves 0.85 Recall@20, adding graph boosts to 0.89.", "timestamp": "2026-03-28T10:30:00Z" },
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_00-00__v12-references-removed.md:238:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/z_archive/006-auto-indexing" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_00-00__v12-references-removed.md:243:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_00-00__v12-references-removed.md:354:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_00-00__v12-references-removed.md:355:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-030.md:128:5. Stage budgets matter more than end-to-end p95 alone; watch lock wait, merge/write, continuity verification, index sync, vector gather, rerank/fusion, and resume fallback.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-030.md:142:`write.stage.lock_wait_ms`, `write.stage.merge_write_ms`, `write.stage.continuity_verify_ms`, `write.stage.index_sync_ms`, `read.stage.vector_ms`, `read.stage.fusion_ms`, `read.stage.filter_ms`, `resume.stage.wrapper_ms`, `resume.stage.handover_ms`, `resume.stage.continuity_ms`, `resume.stage.fallback_ms`, `budget_burn`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-030.md:145:resume p95 `<500ms`, save p95 `<2s`, search p95 `<300ms`, trigger match p95 `<10ms`, archived hit rate `<5%` during the phase-019 monitoring window, embedding warmup `<5s`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/012-query-intelligence/scratch/reaudit-2026-03-23/gpt54-analyst.md:24:Evidence: [embedding-expansion.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts#L65), [embedding-expansion.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts#L155), [embedding-expansion.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/embedding-expansion.ts#L211), [stage1-candidate-gen.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts#L523), [search-flags.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts#L107).
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:158:| `memory_search` - Vector search | ✅ |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:159:| `memory_match_triggers` - Fast matching | ✅ |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:171:**File**: `/Users/michelkerkmeester/MEGA/MCP Servers/semantic-memory/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:216:| `semantic-memory/lib/vector-index.js:497-500` | importanceTier bug fix |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:299:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/z_archive/006-auto-indexing" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:304:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:419:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_12-45__session-complete.md:420:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-020.md:34:- [ ] Verify embedding runtime is healthy (no warmup timeouts)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/068-constitutional-readme-fix/scratch/legacy-memory-quarantine/16-01-26_09-05__constitutional-readme-fix.md:252:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/068-constitutional-readme-fix" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/068-constitutional-readme-fix/scratch/legacy-memory-quarantine/16-01-26_09-05__constitutional-readme-fix.md:257:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/068-constitutional-readme-fix/scratch/legacy-memory-quarantine/16-01-26_09-05__constitutional-readme-fix.md:377:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/068-constitutional-readme-fix/scratch/legacy-memory-quarantine/16-01-26_09-05__constitutional-readme-fix.md:378:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-45__docs-alignment-complete.md:152:   - Updated memory_search parameters (tier, contextType, useDecay, includeContiguity, includeConstitutional)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-45__docs-alignment-complete.md:198:- memory_search, memory_load, memory_match_triggers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-45__docs-alignment-complete.md:312:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "** specs/005-memory/004-auto-indexing" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-45__docs-alignment-complete.md:317:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-45__docs-alignment-complete.md:433:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_11-45__docs-alignment-complete.md:434:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-017.md:76:| `memory-pipeline-regressions.vitest.ts` | Title truncation, trigger phrase filtering, embeddings | Both | Partial -- mode-agnostic |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-017.md:123:- `mcp_server/tests/` files: these cover MCP handler tests (memory_save, memory_search), not the generate-context CLI pipeline.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/spec.md:3:description: "Read-only 20-iteration research investigation of the Claudest external Claude Code plugin marketplace and the claude-memory plugin (FTS5/BM25 conversation recall, SessionStart context injection, extract-learnings consolidation, get-token-insights observability) to identify adopt/prototype/reject patterns and execution-ready follow-on packet contracts for Code_Environment/Public's Spec Kit Memory and Code Graph stack."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/spec.md:30:Phase 5 of `001-research-graph-context-systems` is a read-only audit of the Claudest external Claude Code plugin marketplace (`external/.claude-plugin/marketplace.json`) and its flagship `claude-memory` plugin to translate concrete patterns into actionable improvements for `Code_Environment/Public`. The plugin is studied at function level: the v3 SQLite schema with branch-aware BM25/FTS5 recall, the Stop/SessionStart hook chain that pre-computes branch summaries and injects them into the next session via `hookSpecificOutput.additionalContext`, the `extract-learnings` consolidation pipeline split between `memory-auditor` and `signal-discoverer`, and the `get-token-insights` skill that ingests Claude JSONL session logs into a relational analytics model with embedded HTML dashboard. The deliverable is an evidence-grounded `adopt now` / `prototype later` / `reject` matrix grounded in `external/plugins/...` file:line citations across 20 deep-research iterations, plus packet-ready briefs and an execution-ready follow-on packet roadmap for Public's FTS, analytics, SessionStart, and consolidation seams.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/spec.md:62:`Code_Environment/Public` already has Spec Kit Memory MCP (semantic search, intent-aware routing, importance tiers), Code Graph for structural queries, the `024/002` SessionStart hook for source-aware routing, and the `024/003` Stop hook for token snapshots and session summaries. But Public lacks (a) a runtime FTS capability cascade that degrades from FTS5/BM25 → FTS4 → LIKE rather than failing silently when the SQLite build varies, (b) a Stop-time pre-computed `context_summary` cached on per-session state for SessionStart fast-path injection, (c) an explicit auditor-vs-discoverer split in its consolidation flow, and (d) cross-session analytics-grade storage with cache-tier-aware pricing normalization. Without an evidence-grounded survey of how Claudest's `claude-memory` plugin actually implements these patterns at function level, any port would risk importing the wrong patterns or missing the load-bearing implementation nuances.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/spec.md:79:- BM25/FTS5 → FTS4 → LIKE recall cascade in `external/plugins/claude-memory/skills/recall-conversations/scripts/search_conversations.py`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/spec.md:112:| REQ-002 | P0 | Map the v3 SQLite schema in `db.py` (projects/sessions/branches/messages/branch_messages/import_log + `branches_fts`/`messages_fts`) and explain why branch-level aggregation matters for BM25 ranking |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/spec.md:250:- **Then** the iteration file documents the FTS5 BM25 ranking branch, the FTS4 MATCH+recency branch, and the LIKE %term% branch with line citations and explicit query rewriting rules
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/012-query-intelligence/implementation-summary.md:43:All 11 query intelligence features were audited — complexity routing, score fusion, channel enforcement, confidence truncation, token budgets, query expansion, LLM reformulation, HyDE, surrogates, decomposition, and graph concept routing. All 11 are now fully documented after catalog remediation on 2026-03-26.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/012-query-intelligence/implementation-summary.md:51:1. Complexity router, RSF shadow, channel-min-rep, confidence truncation, token budget, query expansion, decomposition, graph concept routing: all MATCH
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-005.md:111:When the user needs deeper context (e.g., `memory_context(deep)`):
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-005.md:139:- The embedding of `recent_action + next_safe_action` (for semantic resume queries)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-005.md:160:- **F5.4**: Resume latency target <100ms is achievable with YAML parse of a small block. No SQLite query, no embedding compute, no LLM call on the happy path.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-005.md:171:| 2 | Content routing rules | 8 content categories, 3-tier classifier (rule → embedding → LLM) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_13-30__command-alignment.md:296:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/z_archive/006-auto-indexing" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_13-30__command-alignment.md:301:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_13-30__command-alignment.md:416:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-25_13-30__command-alignment.md:417:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/plan.md:41:Run a 20-iteration deep-research loop against `external/` to translate Claudest's claude-memory plugin (v3 SQLite schema with branch-aware BM25/FTS5 recall, Stop/SessionStart hook chain with cached `context_summary` fast path, `extract-learnings` consolidation with `memory-auditor`/`signal-discoverer` split) and the `get-token-insights` skill into Public-actionable adopt/prototype/reject recommendations, packet-ready briefs, and implementation-ready follow-on contracts. Iterations 1-12 dispatched through `cli-codex gpt-5.4 high --full-auto --sandbox workspace-write`; iteration 7 converged the original charter, then iterations 8-12 deepened Q10 into matrix, sequencing, v1 slicing, packet briefs, and uncertainty closeout. The packet was then reopened in `completed-continue` mode for iterations 13-20, which converted the first continuation into concrete implementation seams: FTS capability helper scope, forced-degrade tests, Stop-hook metadata patch, normalized analytics replay schema, SessionStart fast-path placement, verifier/discoverer split mapping, portable token-observability contracts, and a dependency-ordered roadmap. Externalized state in `research/deep-research-{config,state,strategy,dashboard,findings-registry}` survives crash and resume; reducer runs after every iteration to keep registry, dashboard, and machine-owned strategy sections in sync.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/plan.md:188:- **Memory persistence**: Saved memory artifacts must persist cleanly in `memory/`; if the current indexing policy skips semantic indexing, the docs must state that honestly rather than claiming embedding success.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/plan.md:203:- Voyage API key for memory embedding (`VOYAGE_API_KEY` env var).
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-018.md:148:6. **Embedding input:** The final rendered markdown (potentially 10K+ chars just from SUMMARY) is sent to the embedding provider. Very long documents may: (a) exceed embedding model token limits (voyage-4: 32K tokens), (b) dilute embedding relevance signal as the summary dominates the vector.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-018.md:159:**Risk Level:** MEDIUM -- Does not break the pipeline but produces suboptimal memories. The quality scorer does not penalize length. The sufficiency gate does not check for excessive length. The main damage is retrieval inefficiency: a 10K-char memory uses disproportionate context window budget when surfaced by `memory_search`.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-018.md:192:- **Embedding relevance:** 100+ file paths will dominate the embedding vector, reducing relevance for semantic queries about the actual session content
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/012-memory-save-quality-pipeline/research/iterations/iteration-018.md:202:**Risk Level:** HIGH -- 100+ file entries create oversized memories with diluted embeddings and potential contamination false-positives. The placeholder descriptions provide no semantic value while consuming token budget.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:252:| Search | `memory_search()` | ❌ ERROR | `no such column: m.importance_tier` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:274:**1. Database Schema Migration** (`vector-index.js`)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:298:| `vector-index.js` | `/Users/michelkerkmeester/MEGA/MCP Servers/semantic-memory/lib/` | Added migration for 10 missing columns |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:309:| Trigger Match | `memory_match_triggers()` | ✅ Working | Fast phrase matching (<50ms) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:311:| **Search** | `memory_search()` | ✅ **FIXED** | Vector search with tier filtering |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:380:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "** `specs/005-memory/004-auto-indexing`" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:385:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:496:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/scratch/legacy-memory-quarantine/16-12-24_00-00__memory-docs-cleanup.md:497:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:2:title: "Iteration 021 — Classifier prototype library for Tier 2 embedding similarity"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:9:focus: "Populate the Tier 2 prototype library with concrete sample chunks for all 8 routing categories so ambiguous saves can fall back to nearest-neighbor embedding classification."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:26:Iteration 002 fixed the classifier architecture but left the Tier 2 prototype corpus open. This pass fills that gap. The aim is not to invent abstract labels; it is to give the embedding layer 40 realistic, high-signal chunks shaped like this repo's actual `implementation-summary.md`, `decision-record.md`, `handover.md`, `research/research.md`, `tasks.md`, and legacy `memory/*.md` artifacts. Per iteration 002, this library supports the 15% of chunks that Tier 1 rules cannot classify confidently. Per phase 017 seed F4 and phase 017 iteration 004, the most important boundary is not "good prose vs bad prose"; it is "canonical narrative vs thin metadata vs drop-worthy boilerplate/noise."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:30:Below, each prototype is a normalized sample chunk derived from real repo patterns, not a verbatim lift. The label notes the shape the embedding should learn.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:44:- `ND-03 staged runtime remediation`: "Attempt 1 confirmed that `memory_search(\"semantic search\")` returned results again, but Attempt 2 kept the work in a pending state until the MCP server could be restarted and the new focused-mode fix rechecked in a fresh session. The implementation was compiled before handover, yet the delivery story deliberately stopped at 'awaiting runtime verification after restart.' That phrasing belongs in `how-delivered`, not `what-built`."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:67:- `RF-02 architecture conclusion`: "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, not a build story or ADR."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:91:- `DR-02 recovery hints boilerplate`: "Recovery scenarios: Context Loss -> run `/spec_kit: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. It is not packet-specific knowledge and should not consume canonical doc space."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:103:- `embeddingProfile`: symbolic name for "use the same embedding pipeline as ambiguous save chunks"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:114:The important implementation detail is not the path alone; it is that the library stays human-editable, versioned with the router, and stable enough that embedding refreshes can be regenerated deterministically.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-021.md:137:- The best `decision` prototypes are not just "we chose" sentences. They also include alternatives, consequences, checks, and rollback language, which gives the embedding space more texture than a one-line rationale would.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/021-memory-choice-enforcement/scratch/legacy-memory-quarantine/17-12-25_08-08__memory-choice-enforcement.md:412:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "005-memory/011-memory-choice-enforcement" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/021-memory-choice-enforcement/scratch/legacy-memory-quarantine/17-12-25_08-08__memory-choice-enforcement.md:417:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/021-memory-choice-enforcement/scratch/legacy-memory-quarantine/17-12-25_08-08__memory-choice-enforcement.md:536:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/021-memory-choice-enforcement/scratch/legacy-memory-quarantine/17-12-25_08-08__memory-choice-enforcement.md:537:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:9:You are a specialist in Claude Code plugin marketplace architecture, conversation memory systems with FTS5/BM25 ranking, learning extraction pipelines, and token-usage observability tooling.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:32:`claude-memory` combines automatic session recall, branch-aware SQLite storage, and a memory hierarchy that flows from global `CLAUDE.md` to repo `CLAUDE.md` to `MEMORY.md` and detailed topic files. Its storage layer uses SQLite with FTS5 and BM25 when available, FTS4 or `LIKE` fallback otherwise, and caches pre-rendered session summaries in the `branches` table so SessionStart injection becomes a fast lookup instead of replaying raw transcripts. The main user-facing surfaces are automatic context injection, `recall-conversations`, and `extract-learnings`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:48:`Code_Environment/Public` already has Spec Kit Memory with `memory_search`, session continuity, `generate-context.js` for structured memory saves, an agent-facing `MEMORY.md` pattern, and importance tiers in frontmatter. It also already has `.opencode/skills/` as its own plugin-like skill distribution surface.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:60:7. Read the recall layer next: `skills/recall-conversations/SKILL.md`, `scripts/search_conversations.py`, and `scripts/recent_chats.py`. Capture the actual query interface, BM25 usage, project filtering, and fallback behavior.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:72:    Research the external repository at /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-graph-context-systems/005-claudest/external and identify concrete improvements for Code_Environment/Public, especially around Claude Code plugin marketplace structure, conversation memory with FTS5/BM25 ranking, automatic context injection on session start, learning extraction with batch-processing agents, and token-usage observability dashboards.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:82:2. What does the `claude-memory` SQLite schema actually store in `projects`, `sessions`, `branches`, `messages`, `branch_messages`, and FTS tables, and why is branch-level aggregation important for BM25-ranked recall?
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:84:4. How does `recall-conversations` expose search and chronological browsing, and what does its BM25/FTS5 -> FTS4 -> `LIKE` cascade imply for portability and ranking quality?
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/scratch/phase-research-prompt.md:147:- FTS5/BM25 conversation recall
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/fix-summary.md:13:**Component**: `vector-index.js` → `updateMemory()`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/fix-summary.md:16:The `memory_update` MCP tool accepted `importanceTier` as a parameter but the `updateMemory()` function in `vector-index.js` didn't process it. The tier value was silently ignored.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/fix-summary.md:22:`/Users/michelkerkmeester/MEGA/MCP Servers/semantic-memory/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/fix-summary.md:41:if (embedding) {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/fix-summary.md:54:if (embedding) {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/fix-summary.md:136:- [x] Bug fix applied to `vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/006-auto-indexing/fix-summary.md:150:| `semantic-memory/lib/vector-index.js` | Bug fix (lines 497-500) |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/022-implement-and-remove-deprecated-features/implementation-summary.md:111:| **Source Files** | `shared/embeddings.ts`, `mcp_server/context-server.ts`, `mcp_server/lib/eval/shadow-scoring.ts`, `mcp_server/lib/scoring/composite-scoring.ts`, `mcp_server/lib/search/hybrid-search.ts` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/decision-record.md:297:- `handleMemoryUpdate()` - metadata + embedding update
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/decision-record.md:340:| `vector-index.js:deleteMemory` | Delete history → delete vector → delete memory |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/decision-record.md:341:| `context-server.js:handleMemoryUpdate` | Update metadata → regenerate embedding |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/decision-record.md:441:Current LRU cache in `vector-index.js` uses O(n) eviction by iterating all entries to find the oldest. With 500 entry limit, this adds latency.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/022-implement-and-remove-deprecated-features/graph-metadata.json:49:      "shared/embeddings.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/022-implement-and-remove-deprecated-features/graph-metadata.json:92:        "name": "embeddings.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/022-implement-and-remove-deprecated-features/graph-metadata.json:94:        "path": "shared/embeddings.ts",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-035.md:30:I did not find a standalone `schema.sql` for `causal_edges` in the prompt-suggested paths. The live source of truth is `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:605-635,937-947`, with tests confirming the same shape at `.opencode/skills/system-spec-kit/mcp_server/tests/causal-edges.vitest.ts:68-80,500-527`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-035.md:45:Neighbor identity already exists in `memory_index(spec_folder, file_path, anchor_id)` with `UNIQUE(spec_folder, file_path, anchor_id)`. Source: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2297-2358`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/002-skill-graph-daemon-native-advisor-tools/research/findings-registry.json:21:    {"id": "B2", "track": "B", "title": "Extraction pipeline", "verdict": "adopt_now", "confidence": "high", "iteration": 10, "rationale": "Adopt a deterministic hybrid pipeline with explicit signals, TypeScript n-gram/pattern extraction, and corpus-aware DF/IDF; keep embeddings offline or prototype-only.", "evidence": ["iterations/iteration-010.md:6", "iterations/iteration-010.md:42", "iterations/iteration-010.md:51"]},
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/002-skill-graph-daemon-native-advisor-tools/research/findings-registry.json:32:    {"id": "C6", "track": "C", "title": "Performance", "verdict": "prototype_later", "confidence": "high", "iteration": 21, "rationale": "Do not adopt prompt-time embedding lookup on every advisor prompt now; keep exact cache, lexical, and skill-graph SQL work in the hot path.", "evidence": ["iterations/iteration-021.md:6", "iterations/iteration-021.md:39", "iterations/iteration-021.md:48"]},
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/002-skill-graph-daemon-native-advisor-tools/research/findings-registry.json:34:    {"id": "C8", "track": "C", "title": "Target accuracy", "verdict": "adopt_now", "confidence": "high", "iteration": 23, "rationale": "Adopt 70% full-corpus and holdout top-1 gates for deterministic improvements, with stricter gates for prompt-time embedding or learned scoring.", "evidence": ["iterations/iteration-023.md:6", "iterations/iteration-023.md:35", "iterations/iteration-023.md:53"]},
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/plan.md:36:| **Storage** | better-sqlite3, vector embeddings |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:120:- **Location:** `vector-index.js:2824-2848`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:131:- **Requirement:** Metadata update MUST rollback if embedding regeneration fails
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:133:- **Behavior:** Wrap in transaction, rollback on embedding failure
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:134:- **Validation:** Force embedding failure, verify metadata unchanged
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:197:- **Location:** `vector-index.js:714`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:202:- **Location:** `vector-index.js:2329`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:208:- **Location:** `vector-index.js:923-939`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:281:| C2 | CRITICAL | Memory | vector-index.js | 2824-2848 | No orphaned file detection |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:289:| H4 | HIGH | Memory | context-server.js | 981-1004 | Partial embedding update |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:290:| H5 | HIGH | Database | vector-index.js | 714 | Missing index |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:291:| H6 | HIGH | Database | vector-index.js | 2329 | Timestamp format |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/spec.md:292:| H7 | HIGH | Database | vector-index.js | 923-939 | No cascade delete |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/implementation-summary.md:83:3. **Branch-aware BM25 is the load-bearing recall pattern** — the v3 schema stores messages once and treats branches as a separate index with `aggregated_content` + `context_summary`. BM25 ranks whole branches, then hydration recovers exact message sequences. (iter 2)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/implementation-summary.md:96:- **Adopt now**: branch-aware BM25/FTS5 cascade (probe-first, explicit query branches), cached-summary SessionStart fast path (Stop-time write + SessionStart read augmentation), auditor/discoverer split for consolidation, cache-cliff metric, per-tier pricing/cache cost normalization, dashboard JSON contracts (`trends`, `skill_usage`, `agent_delegation`, `hook_performance`, `findings`, `recommendations`).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/implementation-summary.md:180:- **`fts4_match` lane is gated on schema work**: The Brief A v1 was narrowed to `fts5_bm25 → like_scan` because Public still provisions only `memory_fts USING fts5` (`mcp_server/lib/search/vector-index-schema.ts:2382-2412`). Restoring an `fts4_match` lane requires alternate FTS4 schema creation in the same packet.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/012-command-alignment/implementation-summary.md:77:| `/memory:search` | `memory_context`, `memory_quick_search`, `memory_search`, `memory_match_triggers`, `task_preflight`, `task_postflight`, `memory_drift_why`, `memory_causal_link`, `memory_causal_stats`, `memory_causal_unlink`, `eval_run_ablation`, `eval_reporting_dashboard`, `memory_get_learning_history` | L1, L2, L6, L7 |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:57:│ Caller → memory_context (handler)                    │
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:61:│    → 4-stage pipeline: gather → score → rerank → filter│
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:62:│    → RRF fusion across vector/bm25/fts5/graph/trigger│
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:72:│    → memory_context({ mode: "resume", profile: "resume" })│
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:74:│    → adds code-graph + CocoIndex state              │
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:111:│ Caller → memory_context (retargeted)                 │
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:127:│    3. Query spec docs via memory_context(spec_doc)   │
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:141:| Resume first-hit | `memory_context(resume)` | `handover.md` read | Rewrite (different source) |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-001.md:186:Design `contentRouter`. Enumerate the 8 content categories. Propose a classifier contract (rule-based vs embedding vs LLM). Define refuse-to-route and user-override behaviors. Answer Q1 (routing authority).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/005-claudest/graph-metadata.json:213:    "causal_summary": "Phase 5 of `001-research-graph-context-systems` is a read-only audit of the Claudest external Claude Code plugin marketplace (`external/.claude-plugin/marketplace.json`) and its flagship `claude-memory` plugin to translate concrete patterns into actionable improvements for `Code_Environment/Public`. The plugin is studied at function level: the v3 SQLite schema with branch-aware BM25/FTS5 recall, the Stop/SessionStart hook chain that pre-computes branch summaries and injects them into the next session via `hookSpecificOutput.additionalContext`, the `extract-learnings` consolidation pipeline split between `memory-auditor` and `signal-discoverer`, and the `get-token-insights` skill that ingests Claude JSONL session logs into a relational analytics model with embedded HTML dashboard. The deliverable is an evidence-grounded `adopt now` / `prototype later` / `reject` matrix grounded in `external/plugins/...` file:line citations across 20 deep-research iterations, plus packet-ready briefs and an execution-ready follow-on packet roadmap for Public's FTS, analytics, SessionStart, and consolidation seams.",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/002-skill-graph-daemon-native-advisor-tools/research/next-research-paths.md:19:| **C6** | Prompt-time embedding/hybrid lookup | Hot-path latency risk; semantic channels stay shadow-only until promotion gates pass | Need shadow-cycle methodology + promotion-gate tuning before C6 can ever leave `prototype_later` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:79:| C2 | Add orphaned file detection | vector-index.js | 3h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:88:- [ ] Run memory_search, verify no duplicates
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:155:| H5 | Add idx_history_timestamp migration | vector-index.js | 1h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:156:| H6 | Standardize timestamp format | vector-index.js | 2h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:157:| H7 | Implement cascade delete | vector-index.js | 1h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:186:    // Then delete vector
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:196:| H4 | Rollback on embedding failure | context-server.js | 2h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:263:| M5 | Optimize LRU cache eviction | vector-index.js | 2h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:264:| M9 | Handle partial embedding update | context-server.js | 1h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:265:| M10 | Clear constitutional cache on tier change | vector-index.js | 30m |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:267:| M12 | Delete memory_history on memory delete | vector-index.js | (done in H7) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:295:| M19 | Add migration versioning | vector-index.js | 2h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:408:| `vector-index.js` | Orphan detection, cascade delete, indexes, timestamps, LRU | 1, 2, 3 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/plan.md:410:| `context-server.js` | Error codes, embedding rollback | 2 |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-010.md:15:- Hidden late-cycle P0 across the reviewed runtime and doc surfaces: the final pass did not surface any data-loss, auth-bypass, or hard-gate defect beyond the already active P1 set. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:75:- [x] **P0** `memory_search` returns unique results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:82:**File:** `vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:176:**Task:** Rollback metadata on embedding failure
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:182:- [x] **P1** Metadata unchanged after failed embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:188:**File:** `vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:192:  - Evidence: vector-index.js migration added
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:199:**File:** `vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:210:**File:** `vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:288:- [ ] **P2** M9: Partial embedding update handled
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:372:CHK-C2: 2025-12-26 CODE vector-index.js verifyIntegrity() updated with fs.existsSync()
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:385:CHK-H5: 2025-12-26 CODE vector-index.js migration added for idx_history_timestamp
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:399:CHK-M5: 2025-12-26 CODE vector-index.js LRUCache class added with O(1) eviction
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:403:CHK-M10: 2025-12-26 CODE vector-index.js clears constitutional cache on tier change/delete
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:406:CHK-M14: 2025-12-26 CODE vector-index.js logs warnings for vector deletion errors
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/checklist.md:407:CHK-M15: 2025-12-26 CODE context-server.js blocks until embedding model ready
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-004.md:15:- Feature-catalog telemetry and neutral-length notes are stale: the reviewed catalog surfaces correctly describe rerank gating at four rows plus compatibility-only length scaling and telemetry counters. [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/01--retrieval/05-4-stage-pipeline-architecture.md:25`] [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/feature_catalog.md:241`]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/076-post-speckit-template-upgrade-command-allignment/implementation-summary.md:102:| spec_kit/assets | 14 | Version refs, missing Level 1 file, memory_search params |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/076-post-speckit-template-upgrade-command-allignment/implementation-summary.md:120:| memory_search params | Missing query, no anchors | `query`, `specFolder`, `anchors: ['summary', 'state', 'next-steps']` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/076-post-speckit-template-upgrade-command-allignment/implementation-summary.md:172:| memory_search has anchors | 2 YAMLs | 2 YAMLs | PASS |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:82:- [ ] `memory_search` returns unique results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:90:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:95:`verifyIntegrity()` only checks vector-to-index consistency but NOT if the referenced files actually exist on the filesystem. Deleted files remain in database indefinitely.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:351:When embedding regeneration fails after title change, metadata still updates but search is stale.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:358:  const updateResult = vectorIndex.updateMemory(id, updates);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:360:  // If title changed, regenerate embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:362:    const embedding = await embeddings.generateEmbedding(updates.title);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:363:    if (!embedding) {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:364:      throw new Error('Failed to regenerate embedding');
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:366:    vectorIndex.updateEmbedding(id, embedding);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:374:- [ ] Force embedding failure (mock)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:383:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:417:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:448:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:462:    // 2. Delete vector
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:654:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:719:| M9 | Handle partial embedding update | context-server.js | 1h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:720:| M10 | Clear constitutional cache on tier change | vector-index.js | 30m |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:724:| M14 | Handle vector deletion error in transaction | vector-index.js | 30m |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:729:| M19 | Add migration versioning | vector-index.js | 2h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:756:| L11 | Remove duplicate `last_accessed` column | vector-index.js | 2h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:757:| L12 | Add embedding timeout wrapper | embeddings.js | 1h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:758:| L13 | Add batch embedding API | embeddings.js | 3h |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/046-post-release-refinement-1/tasks.md:759:| L14 | Implement granular cache invalidation | vector-index.js | 2h |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-005.md:11:- **F003**: The `005-doc-surface-alignment` packet records the unshipped continuity Stage 3 lambda as verified reality — `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:65` — the packet spec, tasks, checklist, and implementation summary all say the continuity Stage 3 MMR lambda behavior was verified and documented, but the runtime Stage 3 branch under review still ignores `adaptiveFusionIntent` and does not execute that continuity-aware handoff. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/spec.md:62`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/tasks.md:58`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:65`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/implementation-summary.md:61`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-005.md:14:{"type":"claim-adjudication","findingId":"F003","claim":"The packet-local doc-alignment evidence for phase 005 incorrectly treats the continuity Stage 3 lambda behavior as verified shipped reality.","evidenceRefs":[".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/spec.md:62",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/tasks.md:58",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:65",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/implementation-summary.md:61",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209"],"counterevidenceSought":"Read the packet-local spec, tasks, checklist, and implementation summary alongside the live Stage 3 code looking for a narrower interpretation or a runtime fix that made the packet evidence true; neither was present.","alternativeExplanation":"The packet may have been documenting the intended final state rather than the shipped state, but its completion markers and verification language present the claim as already confirmed reality.","finalSeverity":"P1","confidence":0.9,"downgradeTrigger":"Downgrade if either the runtime Stage 3 continuity handoff lands and the packet evidence becomes true, or the packet is amended to describe the continuity lambda as a deferred/follow-on item.","transitions":[{"iteration":5,"from":null,"to":"P1","reason":"Initial discovery"}]}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-005.md:20:- Phase 005 over-claimed the rerank gate or telemetry surfaces: those parts of the packet remain aligned with the live runtime. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:64`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:66`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/review/iterations/iteration-001.md:25:- Evidence: [SOURCE: .opencode/skills/system-spec-kit/scripts/memory/cleanup-orphaned-vectors.ts:15]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/review/iterations/iteration-001.md:89:- [SOURCE: .opencode/skills/system-spec-kit/scripts/memory/cleanup-orphaned-vectors.ts:15]
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/019-decisions-and-deferrals/scratch/reaudit-2026-03-23/gpt54-cross-cutting.md:32:- Phase 003 F03: document `embeddingRetry`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/019-decisions-and-deferrals/scratch/reaudit-2026-03-23/gpt54-cross-cutting.md:52:- Dead code or dead declarations presented as functional: Phase 013 F21 “merge” behavior; Phase 018 F15 `profile` on `memory_context`; Phase 005 notes dead `rebuildVectorOnUnarchive()` though the catalog was correct there.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-001.md:11:- **F001**: Stage 3 MMR ignores the internal continuity handoff — `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209` — `handleMemorySearch()` maps `profile === 'resume'` to `adaptiveFusionIntent = 'continuity'`, and Stage 1 forwards that internal intent into hybrid search, but Stage 3 still selects its lambda from `config.detectedIntent`. Because `SPECKIT_MMR` defaults to enabled, resume-oriented searches can lose the continuity profile in the final ordering step. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:830`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:538`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:641`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:69`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-001.md:14:{"type":"claim-adjudication","findingId":"F001","claim":"The shipped continuity profile is only partially wired because the default Stage 3 MMR pass still ignores adaptiveFusionIntent and falls back to detectedIntent/default lambda selection.","evidenceRefs":[".opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:830",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:538",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209",".opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:641",".opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:69"],"counterevidenceSought":"Read the handler wiring, Stage 1 handoff, Stage 3 MMR branch, lambda map, and default MMR flag looking for a continuity-aware override or disabled default path; none exists.","alternativeExplanation":"Continuity could have been intended as a Stage 2-only profile, but the phase docs and implementation summary both claim the Stage 3 lambda landed, so the partial handoff is still a real runtime mismatch.","finalSeverity":"P1","confidence":0.93,"downgradeTrigger":"Downgrade if Stage 3 is updated to read adaptiveFusionIntent (or an equivalent continuity-aware override) and a regression test proves resume-profile ordering stays continuity-aware through MMR.","transitions":[{"iteration":1,"from":null,"to":"P1","reason":"Initial discovery"}]}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-001.md:23:- Searching for a hidden continuity-aware Stage 3 override did not surface any alternate path beyond `config.detectedIntent` and `INTENT_LAMBDA_MAP`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-001.md:26:Verify the rest of the shipped runtime surfaces around reranker telemetry, rerank gating, and Tier 3 routing so the continuity defect is isolated cleanly.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:34:- Seed enough data to activate all five search channels: trigger, BM25, FTS5, vector, and graph.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:47:- The only way to find the target is by vector or BM25 search after the trigger path fails.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:191:## Scenario 12 — Embedding semantic search
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:192:- Test name: `embedding_search_returns_expected_top_k_for_retargeted_docs`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:194:- Action: Run an embedding-driven search with a paraphrased query that should succeed on semantics rather than exact token overlap.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:197:- The embedding system covers retargeted document classes the same way it covered legacy memory rows, preserving the Voyage-based semantic path.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:207:- Setup: Build one query fixture where trigger, BM25, FTS5, vector, and graph channels all contribute useful but different evidence for the final answer.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:208:- Action: Run the full search pipeline with trace output enabled so gather, score, rerank, and filter behavior can be inspected end to end.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-025.md:211:- The scoring and reranking stages produce a sensible fused order rather than a single-channel winner that ignores the others.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/spec.md:30:Phase 4 of `001-research-graph-context-systems` is a read-only audit of the graphify external Python skill to translate its two-pass codebase knowledge graph patterns 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 grounded in specific `external/graphify/` file:line citations, 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/004-graphify/spec.md:32:**Key Decisions**: Use a 20-iteration two-wave deep-research loop; preserve K1 to K42 finding lineage across the original run plus completed-continue wave; keep Code Graph MCP and CocoIndex as the platform while translating graphify patterns into additive rollout guidance for Public.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/spec.md:61:Public already has Code Graph MCP for structural code queries (442.9K nodes, 225.4K edges), CocoIndex for semantic retrieval, Spec Kit Memory for persistent context, and hook-based context injection patterns. It does NOT have community-clustered knowledge graphs, multimodal artifact extraction (PDFs, images), evidence-tagged provenance for retrieval edges, or a PreToolUse hook that nudges Claude away from raw Grep when a structural index exists. graphify ships all four capabilities in a small Python package, so it is the closest external candidate to study before deciding which patterns to bring inside Public.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/spec.md:65:Produce an evidence-backed translation layer that tells Public exactly which graphify patterns to adopt directly, adapt into existing surfaces, or reject as duplicative or non-applicable, with every recommendation tied to `external/graphify/` file:line evidence and to a specific Public surface (Code Graph MCP, CocoIndex, Spec Kit Memory, hooks, or CLAUDE.md).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/spec.md:93:- Wholesale replacement of Code Graph MCP or CocoIndex - prompt Don'ts forbid it unless graphify clearly solves something they cannot
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/spec.md:130:| REQ-009 | Compare graphify against Public's existing Code Graph MCP and CocoIndex without duplicating phase 002 or phase 003 findings | research.md section 10 has a capability matrix; section 11 documents cross-phase deduplication |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/spec.md:288:1. **Given** any Adopt row in research/research.md section 12, **When** I read the "Concrete Adoption Plan" column, **Then** I see a specific Public surface (for example `code_graph_query` response payload, project hooks, CocoIndex incremental update path).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-006.md:11:- **F004**: Child packets `001-004` are still open from a checklist-verification standpoint — `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:3` — each of the first four child packets still carries `status: planned` plus unchecked items, so the `001` tree is not actually fully checklist-verified even though runtime work shipped and phase `005` is strict-clean. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:15`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md:15`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/003-continuity-search-profile/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/003-continuity-search-profile/checklist.md:13`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md:13`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-006.md:14:{"type":"claim-adjudication","findingId":"F004","claim":"The 001 packet tree is not fully checklist-verified because child packets 001-004 still carry planned status and unchecked checklist items.","evidenceRefs":[".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:3",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:15",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md:3",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/003-continuity-search-profile/checklist.md:13",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md:13"],"counterevidenceSought":"Read the child task lists and strict-validation summaries looking for a packet-local note that these checklist gaps were intentionally waived or superseded; none was present in the reviewed tree.","alternativeExplanation":"The checklist gaps could be intentional advisory-only leftovers, but the packet tree is being reviewed as complete post-implementation state, so leaving them as planned/unchecked still makes the closure signal inaccurate.","finalSeverity":"P1","confidence":0.88,"downgradeTrigger":"Downgrade if the unchecked items are explicitly deferred with updated packet status and rationale, or if the checklists are completed with evidence and strict validation closure.","transitions":[{"iteration":6,"from":null,"to":"P1","reason":"Initial discovery"}]}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-006.md:20:- Task-list incompleteness: the child `tasks.md` files are all marked `status: complete`; the closure gap is in checklist verification rather than implementation task execution. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/tasks.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-search-routing-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/tasks.md:3`]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:3:description: "The current SpecKit search relies on vector + FTS5 with partial RRF fusion. Comparative analysis of dotmd, seu-claude, and drift systems revealed that multi-engine approaches wi..."
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:35:The current SpecKit search relies on vector + FTS5 with partial RRF fusion. Comparative analysis of dotmd, seu-claude, and drift systems revealed that multi-engine approaches with graph traversal discover relationships that pure vector+keyword searches miss.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:48:**Details**: Implement vector (existing) + BM25 (new via FTS5) + graph traversal (new via SQLite relations) with Reciprocal Rank Fusion. Graph results receive 1.5x weight multiplier. Results appearing in 2+ engines receive 10% convergence bonus.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:56:| **Triple-hybrid + RRF (dotmd)** | Most comprehensive discovery, handles conceptual + exact + relational queries | Higher complexity, requires BM25 + graph implementation | 9/10 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:88:- BM25 index maintenance overhead - Mitigation: Incremental indexing with content hash
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:101:- `lib/search/vector-index.js` - Add BM25 search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:105:**Rollback**: Feature flag `ENABLE_RRF_FUSION=false` falls back to current vector+FTS5 search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:572:- Must enable vector store swapping (e.g., LanceDB to different provider)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:573:- Must enable embedding provider swapping
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:581:**Details**: Define interfaces for vector store and embedding provider. Implement current SQLite/Voyage as default implementations. This enables testing and future provider swaps without full hexagonal scaffolding.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:634:- `lib/search/vector-index.js` - Implement IVectorStore
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:747:3. `memory_save` couples file creation with embedding generation - embedding failure blocks file save
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:749:5. Schema has `embedding_status` column but it's not leveraged for deferred indexing
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:754:- Must not block memory saves due to embedding API failures
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:755:- Must provide graceful degradation with BM25-only search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:756:- Must support background retry for pending embeddings
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:763:**Summary**: Implement defense-in-depth embedding resilience with 4 layers: pre-flight validation, fallback chain, deferred indexing, and retry with backoff.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:767:2. **Fallback chain**: Primary API → Local (nomic-embed-text) → BM25-only; each step logged
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:768:3. **Deferred indexing**: Save memory file with `embedding_status: 'pending'`; searchable via BM25; background retry
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:804:- Zero memory saves blocked by embedding failures
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:805:- Graceful degradation to BM25-only search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:810:- Increased complexity in embedding layer - Mitigation: Clear separation of concerns via provider chain pattern
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:816:| Pending embeddings never complete | M | Alert if pending > 24h; manual retry command |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:817:| BM25-only mode has lower relevance | L | Log when in fallback mode; surface to user |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:824:- `shared/embeddings/factory.js` - Pre-flight validation + fallback chain
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:825:- `shared/embeddings/providers/voyage.js` - Retry logic
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:827:- `database/schema.sql` - v4.2 migration for embedding_status
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:828:- New `lib/jobs/embedding-retry.js` - Background retry
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/decision-record.md:844:| Q3 | Cross-encoder selection: which provider? | Configurable (Voyage rerank-2 recommended) | Better performance on code/technical content; other providers supported |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/recommendations.md:29:- **Fix:** Remove duplicate at vector-index.js:1111, keep cached version at :209
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/refinement-plan.md:48:- Lazy embedding provider EXISTS (`shared/embeddings.js` singleton pattern), but uses eager warmup
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/refinement-plan.md:85:- This specification defines 15 P0 blockers (10 original + 5 embedding resilience), 18 P1 requirements, and establishes a unified 11-week implementation roadmap to transform SpecKit...
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/refinement-plan.md:86:+ This specification defines 15 P0 blockers (10 original + 5 embedding resilience), 18 P1 requirements, and establishes a unified 6-7 week implementation roadmap to transform SpecKit...
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/refinement-plan.md:141:- RRF Fusion and BM25 can progress in parallel (Week 2)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/refinement-plan.md:179:- RRF Fusion enhancement and BM25 can progress in parallel (Week 2)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/refinement-plan.md:215:| Dependency task failed | T020 (RRF) failed, blocking T031 (BM25) | Report failure, suggest fix, wait for guidance |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-006.md:28:- **Index**: `idx_trigger_cache_source` (SQLite index on `embedding_status='success'` rows)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-006.md:30:- **Consumer**: `memory_context` routes trigger-shaped queries to this fast path, bypassing the 4-stage search pipeline for common cases
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-006.md:43:  WHERE embedding_status = 'success';
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-006.md:48:  WHERE embedding_status = 'success'
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-006.md:56:**Collision handling**: two docs claiming the same trigger phrase. Resolution: return both, ranked by `importance_tier` + `last_review` recency. The caller (`memory_context`) then picks the best match per intent.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-006.md:77:Iteration 7 — intent routing and `memory_context` modes retarget.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-002.md:1:# Iteration 2: Telemetry, rerank minimum, and Tier 3 save routing landed cleanly
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-002.md:4:Check the other shipped runtime changes named in scope so the active problem set distinguishes the Stage 3 continuity defect from already-correct telemetry, rerank-gate, save-routing, and config behavior.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-002.md:16:- Rerank-threshold drift: Stage 3 still skips reranking below four rows and forwards the compatibility `applyLengthPenalty` flag without reintroducing length-based scoring. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:321`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:383`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-002.md:23:Compare the shipped doc surfaces against the live Stage 3 code path, especially where they now mention continuity-specific reranking behavior.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/decision-record.md:135:- `sqliteVecAvailable: vectorIndex.isVectorSearchAvailable()`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/decision-record.md:136:- `vectorSearchEnabled: vectorIndex.isVectorSearchAvailable()`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/decision-record.md:153:| P3-005 | Partial | embedding_status not tracked |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/review/iterations/iteration-012.md:1:# Review Iteration 012: D5 Performance — vector and CLI retest
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/review/iterations/iteration-012.md:4:D5 Performance — vector and CLI retest
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/review/iterations/iteration-012.md:34:- Dimensions addressed: D5 Performance — vector and CLI retest
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:30:Reciprocal Rank Fusion (RRF) combines results from multiple search engines (vector, BM25, graph) into a unified ranked list. Uses the formula `score = weight / (k + rank + 1)` with k=60 as the fusion constant. Results appearing in multiple engines receive a 10% convergence bonus.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:33:SpecKit has `mcp_server/lib/search/rrf-fusion.js` with k=60 and 10% convergence bonus already implemented. However, it's not fully integrated into the search pipeline - vector and FTS5 results are combined but graph traversal is not yet included in the fusion.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:36:Triple-hybrid search with weighted fusion. Vector (1.0x), BM25 (1.0x), and Graph (1.5x) results merge via RRF. Cross-source results get 10% boost. Single ranked output regardless of which engine found what.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:39:- `mcp_server/lib/search/vector-index.js` - Major rewrite
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:41:- All `memory_search` calls - Different ranking behavior
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:46:### Feature 2: BM25 Hybrid Search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:49:Adds proper BM25 (Best Match 25) keyword scoring alongside vector search. BM25 excels at exact term matching, acronyms, and technical identifiers that semantic search misses.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:52:FTS5 is used but not with proper BM25 weighting. Keyword matches are not optimally scored. Technical terms like "FSRS" or "RRF" may not surface correctly.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:55:True BM25 scoring with configurable k1 (1.5) and b (0.75) parameters. Option for WASM-accelerated implementation (5-10x faster) with pure JS fallback. Feeds into RRF fusion pipeline.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:59:- Schema changes for BM25 index storage
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:68:After initial retrieval, sends top-20 candidates to a cross-encoder model for precision reranking. Cross-encoders see query+document pairs together, enabling deeper semantic matching. Supports multiple providers (e.g., Voyage rerank-2, Cohere, or local models).
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:71:No reranking. Initial retrieval order is final. Bi-encoder (embedding) similarity is the only semantic signal.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:74:Optional two-stage retrieval: fast initial search → precise cross-encoder rerank. Includes length penalty (short content <100 chars gets 0.8-1.0x penalty) to prevent low-information snippets from ranking artificially high.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:79:- `options.rerank` parameter on search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:422:Defers embedding model initialization until first use. Lazy Singleton pattern: `getEmbeddingProvider()` initializes on first call, returns cached instance thereafter.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:463:### Feature 21: BM25-WASM Implementation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:466:Uses WebAssembly-compiled BM25 for 5-10x faster keyword search. Falls back to pure JavaScript if WASM unavailable.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:469:FTS5 only. No optimized BM25 implementation.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:473:function createBM25Index() {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:475:    return new BM25Index(); // WASM
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:477:    return new BM25JS();    // Fallback
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:529:  'memory_search': {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:530:    'E041': 'Run memory_index_scan to rebuild vector index',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:531:    'E001': 'Check embedding API key or set SPECKIT_LOCAL_EMBEDDINGS=true',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:549:Comprehensive mapping of all error codes to recovery actions. Covers: memory_search, checkpoint_restore, memory_save, and all other tools.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:629:| L1 | 2000-4000 | memory_context | Unified entry |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:655:  search(embedding: number[], topK: number): Promise<SearchResult[]>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:656:  upsert(id: string, embedding: number[], metadata: object): Promise<void>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:669:Targeted protocol abstractions at integration boundaries. Enables: mock implementations for testing, alternative backends (local vs API embeddings), future LadybugDB migration.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:815:| **Search** | 1-6 | RRF fusion, BM25, cross-encoder, query expansion, intent, graph |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/feature-summary.md:819:| **Performance** | 19-22 | Lazy loading, incremental index, BM25-WASM, compression |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-032.md:94:- 50% anonymized real traffic from `resume`, `memory_context`, `memory_search`, and trigger flows
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-003.md:11:- **F002**: Search docs claim a continuity-aware Stage 3 lambda that the runtime still does not execute — `.opencode/commands/memory/search.md:102` — the command contract, architecture doc, config README, repo README, and feature-catalog summaries now all say the final Stage 3 MMR pass uses continuity lambda `0.65`, but Stage 3 still selects lambda from `config.detectedIntent` rather than the internal continuity handoff used earlier in the pipeline. [SOURCE: `.opencode/commands/memory/search.md:102`] [SOURCE: `.opencode/skills/system-spec-kit/ARCHITECTURE.md:150`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/configs/README.md:49`] [SOURCE: `README.md:393`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-003.md:14:{"type":"claim-adjudication","findingId":"F002","claim":"The updated search docs overstate current reality by documenting a continuity-aware Stage 3 MMR lambda that the live runtime still does not execute.","evidenceRefs":[".opencode/commands/memory/search.md:102",".opencode/skills/system-spec-kit/ARCHITECTURE.md:150",".opencode/skills/system-spec-kit/mcp_server/configs/README.md:49","README.md:393",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209"],"counterevidenceSought":"Read the named doc surfaces plus the live Stage 3 branch looking for wording that scoped continuity to Stage 2 only or a runtime override that made the docs true; neither exists.","alternativeExplanation":"The docs could have intended continuity lambda language as future-state guidance, but the packet is framed as doc alignment to shipped behavior, so presenting it as current reality is still inaccurate.","finalSeverity":"P1","confidence":0.91,"downgradeTrigger":"Downgrade if either the runtime Stage 3 handoff is fixed to match the docs or the docs are corrected to describe continuity as Stage 1/2-only until that fix lands.","transitions":[{"iteration":3,"from":null,"to":"P1","reason":"Initial discovery"}]}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-003.md:20:- `SKILL.md` drift on this exact point: the skill-level search summary is broad about continuity, rerank gating, and telemetry, but it does not explicitly promise the continuity Stage 3 lambda is already active. [SOURCE: `.opencode/skills/system-spec-kit/SKILL.md:592`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/spec.md:92:- External Project graph persistence and query model: LadybugDB adapter, schema, hybrid BM25/vector search, Cypher escape hatch, staleness handling, and registry behavior.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/spec.md:144:| REQ-012 | Runtime and storage assumptions compared | Research compares External Project LadybugDB, embeddings, registry, and MCP assumptions with Public's current runtime constraints |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/spec.md:216:- **RQ-11 Runtime Fit**: Which External Project pieces depend on LadybugDB, embeddings, Tree-sitter native bindings, or project-local install assumptions that do not fit Public?
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/scratch/phase-research-prompt.md:44:- CocoIndex for semantic retrieval over code.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/scratch/phase-research-prompt.md:68:11. Explicitly compare graphify against this repo's existing Code Graph MCP and CocoIndex capabilities so the recommendation set avoids duplicating features already present.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/scratch/phase-research-prompt.md:89:12. Which graphify ideas should be adopted directly, adapted into existing MCP surfaces, or rejected because Public already covers the problem with Code Graph MCP or CocoIndex?
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/scratch/phase-research-prompt.md:108:- Don't propose replacing Code Graph MCP or CocoIndex unless the graph-based alternative clearly solves something they cannot.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/scratch/phase-research-prompt.md:161:- A comparison section that maps graphify capabilities against Public's existing Code Graph MCP and CocoIndex surfaces.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/spec.md:123:| FR-014 | Checkpoint restore preserves embeddings | P1 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:24:SpecKit Reimagined synthesizes findings from 25 parallel agent analyses of 8 pre-analysis documents examining dotmd, seu-claude, drift, and system-speckit architectures. This specification defines 15 P0 blockers (10 original + 5 embedding resilience), 18 P1 requirements, and establishes a unified 6-7 week implementation roadmap to transform SpecKit into a best-in-class memory system with hybrid search, causal graphs, embedding resilience, and self-improvement capabilities.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:28:**Key Decisions**: Adopt drift's session deduplication + type-specific half-lives, enhance dotmd's RRF fusion with convergence bonus, maintain SpecKit's ANCHOR format for token efficiency, and implement defense-in-depth embedding resilience (ADR-009).
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:30:**Critical Dependencies**: Session deduplication (blocks token savings), causal graph (prerequisite for "why" queries), embedding fallback chain (blocks memory save reliability). Note: Lazy loading and RRF fusion foundations already exist in codebase.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:55:- Lazy embedding provider EXISTS (`shared/embeddings.js` singleton pattern), but uses eager warmup
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:70:Transform SpecKit into a self-improving memory system with hybrid search (vector + BM25 + graph), session deduplication, causal lineage tracking, and multi-factor decay scoring, achieving 40-50% relevance improvement and 50% token reduction on follow-up queries.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:81:- P0 (new): Length penalty in reranking, recovery hints catalog, 5-state memory model
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:82:- P1: RRF search fusion, causal memory graph, cross-encoder reranking, BM25 hybrid search, learning from corrections, crash recovery, multi-factor decay, query expansion, standardized response structure, layered tool organization, protocol abstractions, consolidation pipeline
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:83:- P1 (new): Incremental indexing, pre-flight quality gates, CONTINUE_SESSION.md, corrections tracking, fuzzy acronym matching, BM25-WASM
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:97:| `mcp_server/lib/search/vector-index.js` | Modify | Add RRF fusion, BM25 integration |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:132:| "continue [spec name]" | Surface relevant context via memory_search | Gate 2 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:170:| REQ-009 | Recovery Hints Catalog | Complete error-to-hint mapping for memory_search, checkpoint_restore, memory_save |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:179:| REQ-013 | Cross-Encoder Reranking | Top-20 reranking via configurable cross-encoder (e.g., Voyage, Cohere); precision improvement |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:180:| REQ-014 | BM25 Hybrid Search | FTS5 + vector combination in RRF |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:194:| REQ-028 | BM25-WASM Implementation | 5-10x faster BM25 with pure JS fallback |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:201:| REQ-030 | Fallback Embedding Provider Chain | Ordered fallback: Primary API → Local (nomic-embed-text) → BM25-only mode; each step logged with reason |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:202:| REQ-031 | Deferred Indexing on Embedding Failure | Memory saved with `embedding_status: 'pending'`; searchable via BM25/FTS5; background retry when provider available |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:240:| Dependency | RRF implementation | Required before cross-encoder reranking | Phase 2 prerequisite |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:253:- **NFR-P03**: Cross-encoder reranking P95 <500ms (or disable)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:263:- **NFR-R02**: Graceful degradation when embedding API unavailable
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:264:- **NFR-R03**: Embedding provider failures must not block memory saves; deferred indexing with `embedding_status: 'pending'`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:278:- Zero search results: Suggest query expansion or broader anchors
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:282:- Embedding API failure: Fall back to BM25-only search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:283:- Cross-encoder timeout: Skip reranking, return RRF results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:290:- **All providers fail**: Save memory file with `embedding_status: 'failed'`; searchable via BM25; surface warning in memory_save response
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:291:- **Local model unavailable**: Skip to BM25-only mode; log E052 with instructions for installing nomic-embed-text
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:292:- **Partial embedding failure**: Retry failed chunks up to 3x; if still failing, save with `embedding_status: 'partial'`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:293:- **Network timeout during embedding**: Apply 30s timeout per request; trigger fallback after 2 consecutive timeouts
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:304:| Risk | 20/25 | Auth: N, API: Y (embedding, reranking), Breaking: Y (schema v5) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:307:| Coordination | 13/15 | Dependencies: 5 (RRF→rerank, types→decay, lazy→startup, etc.) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:325:| R-009 | Embedding API single-provider dependency | Medium | Medium | Fallback chain: Primary API → Local → BM25-only; IEmbeddingProvider interface for swapping |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:328:| R-009-C | Memory save fails due to embedding failure | High | Medium | Deferred indexing: save file with `embedding_status: 'pending'`; BM25-searchable immediately |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:400:- Defined 15 P0 requirements (10 core + 5 embedding resilience)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:412:- Updated P0 requirement count from 10 to 15 to include embedding resilience
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:428:| Q3 | Cross-encoder selection: which provider? | Infra | Configurable; Voyage rerank-2 recommended for code/technical |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:475:| P1 | Deferred Indexing docs | Graceful degradation when embedding fails |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/spec.md:494:3. **All spec files**: Made embedding-provider agnostic (17 changes across 7 files)
./.opencode/changelog/04--commands/v2.6.1.0.md:3:Integrated CocoIndex search by meaning instead of exact words across spec_kit and create commands, remediated all P1+P2 findings from the 012 command alignment deep review, and folded in the command README rewrite wave from spec 033 plus its same-day punctuation cleanup. The main changes here are semantic search in commands and code search routing table.
./.opencode/changelog/04--commands/v2.6.1.0.md:8:- What changed: Integrated mcp__cocoindex_code__search into spec_kit planning (step 5 explorer agents) and create commands for concept-based code discovery.
./.opencode/changelog/04--commands/v2.6.1.0.md:16:- What changed: Added CocoIndex as first-choice tool for concept/intent queries in the planning phase parallel dispatch configuration.
./.opencode/changelog/04--commands/v2.6.1.0.md:58:| `.opencode/commands/spec_kit/plan.md` | Modified | CocoIndex search routing |
./.opencode/changelog/04--commands/v2.6.1.0.md:61:| `.opencode/commands/create/changelog.md` | Modified | CocoIndex integration |
./.opencode/changelog/04--commands/v2.6.1.0.md:73:- No migration required. Pull latest if you want the CocoIndex-aware command surface and the rewritten Markdown READMEs together.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/plan.md:83:| P1-012 | Include embeddings in checkpoint snapshots | 2h | Phase 1 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/plan.md:88:- [ ] Checkpoint restore preserves semantic search capability
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/plan.md:142:  └── P1-012 (checkpoint embeddings) ───────────────┤
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-022.md:149:3. Run two checks: hard-negative rules from iteration 002/021 cues, then embedding similarity against the Tier 2 prototype library.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-022.md:152:6. Emit warning with suggested alternate target; only hard-fail when both rule-based and embedding checks agree the chunk is truly `drop`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-022.md:160:- Pure structured `_memory` writes may bypass embedding checks.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:68:**Rationale:** Avoids over-engineering of full hexagonal architecture while enabling swappable backends for vector store and embedding providers.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:74:- **RRFEngine**: Triple-hybrid search fusion (vector + BM25 + optional graph) with k=60 and convergence bonus
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:76:- **LazyModelLoader**: Singleton pattern for deferred embedding initialization
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:82:  search(embedding: number[], topK: number): Promise<SearchResult[]>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:83:  upsert(id: string, embedding: number[], metadata: object): Promise<void>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:95:Query → QueryExpansion → [Vector|BM25|Graph] parallel search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:124:| 4-5 | Lazy Model Loading | 4-6h | Deferred embedding init |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:132:- [ ] Lazy singleton for embedding provider
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:141:| 2-3 | BM25 Hybrid Search | 5d | FTS5 + vector combination |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:147:- [ ] `rrfFusion()` with vector, BM25, graph weights
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:159:| 5-6 | Cross-Encoder Reranking | 5d | Top-20 reranking |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:213:| SQLite FTS5 | Internal | Green | Cannot implement BM25 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:215:| Cross-encoder (configurable provider) | External | Yellow | Optional - can skip reranking |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:216:| BM25-WASM | External | Green | JS fallback available |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:242:├── RRF Search Fusion ────────┼──► BM25 Hybrid Search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:251:├── Cross-Encoder Reranking ◄───── RRF + BM25 (Phase 2)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:260:| RRF Search Fusion | None | Cross-Encoder, BM25 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:376:│  │ RRF Search       │                    │ BM25 Hybrid         │           │
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:401:│  ┌──────────────────┐◄─── from RRF + BM25                                  │
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:425:| RRF Search Fusion | None | rrfFusion() | Cross-Encoder, BM25 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:449:- RRF Fusion and BM25 can progress in parallel (Week 2)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:460:| M2 | Search Enhanced | +40% relevance, RRF + BM25 working | Week 3 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:520:| Search Agent | RRF + BM25 | vector-index.js, composite-scoring.js |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:540:| W-R | Search/Retrieval | Primary | vector-index.js, rrf-fusion.js, bm25.js | Phase 2 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:552:| SYNC-002 | RRF + BM25 merged | W-R, W-D | Enhanced search validation |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/plan.md:587:  ENABLE_BM25: process.env.SPECKIT_BM25 ?? false,
./.opencode/changelog/04--commands/v2.4.0.0.md:3:Absorbed the retrieval functionality of /memory:context (L1/L2: memory_context, memory_search, memory_match_triggers) into /memory:analyze, creating a single unified command that handles both intent-aware retrieval (default mode) and analysis subcommands (preflight, postflight, causal, ablation, dashboard, etc.). Command count reduced from 7 to 6. The main changes here are the related file merged into the related file and routing model.
./.opencode/changelog/04--commands/v2.4.0.0.md:89:- tool connection tool names are unchanged (memory_context, memory_search, etc.).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/iterations/iteration-009.md:17:- Playbook regression on the inspected reranker scenario: the updated manual-testing surface accurately describes telemetry counters and compatibility-only length scaling without repeating the continuity Stage 3 claim. [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:19`] [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:30`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/implementation-summary.md:3:description: "20 total deep-research iterations across two waves produced 42 consolidated findings (K1 to K42) and a phased rollout translation for Public's Code Graph, CocoIndex, hooks, validation, and scoring surfaces."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/implementation-summary.md:43:You can now point any Public maintainer at `research/research.md` and get a line-grounded translation layer that says exactly which graphify patterns to adopt, adapt, or reject for Code Graph MCP, CocoIndex, Spec Kit Memory, hooks, validation, and scoring surfaces. The audit now covers 20 total iterations across two waves, produced 42 consolidated K-findings (K1 through K42), and answered all 22 research questions. Reading section 12 plus sections 13.A and 13.B gives the full recommendation and rollout set without backfilling assumptions.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/checklist.md:32:- [x] Duplicate function at vector-index.js:1111 REMOVED → Uses wrapper pattern: internal at L209 + public `getConstitutionalMemoriesPublic` at L1199
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/checklist.md:108:- [x] Parameter passed to vectorIndex.vectorSearch() → L690-697
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/checklist.md:109:- [x] vectorSearchWithContiguity() wired up OR alternative implemented
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/checklist.md:155:- [x] restore inserts embeddings correctly → L386-422
./.opencode/changelog/04--commands/v2.6.0.0.md:3:Added mcp__cocoindex_code__search to allowed-tools in all spec_kit and create command files, enhanced parallel explorer agent prompts with CocoIndex-first guidance, added Code Search Routing protocol blocks, and updated all.agents/commands/ matching runtime config files. Agents now prefer search by meaning instead of exact words for concept-based discovery over exact text search pattern guessing. The main changes here are explorer agent prompts enhanced and code search routing block.
./.opencode/changelog/04--commands/v2.6.0.0.md:8:- What changed: All 8 parallel explorer agents (4 in plan, 4 in complete) now explicitly instruct: "Use CocoIndex first for concept-based discovery, exact text search only for exact known tokens".
./.opencode/changelog/04--commands/v2.6.0.0.md:16:- What changed: Reusable routing table added to the related file and the related file showing when to use CocoIndex vs exact text search vs file-pattern search vs memory_search.
./.opencode/changelog/04--commands/v2.6.0.0.md:24:- What changed: tools: and mcp_servers: arrays updated in all 4 deep-research workflow config variants to include CocoIndex.
./.opencode/changelog/04--commands/v2.6.0.0.md:32:- What changed: Debug sub-agent dispatch template now includes CocoIndex guidance for finding similar working patterns.
./.opencode/changelog/04--commands/v2.6.0.0.md:40:- What changed: Added mcp__cocoindex_code__search to 7 spec_kit.md files (plan, complete, implement, deep-research, debug, phase, resume).
./.opencode/changelog/04--commands/v2.6.0.0.md:48:- What changed: Added mcp__cocoindex_code__search to all 7 create.md files (sk-skill, feature-catalog, testing-playbook, agent, changelog, folder_readme, prompt).
./.opencode/changelog/04--commands/v2.6.0.0.md:56:- What changed: Added CocoIndex discovery guidance to request_analysis_framework in all 12 create workflow config files (6 auto + 6 confirm).
./.opencode/changelog/04--commands/v2.6.0.0.md:64:- What changed: Updated allowed-tools in all 14 applicable runtime config command mirrors (6 spec_kit + 7 create + 1 deep-research) to include mcp__cocoindex_code__search.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-state.jsonl:2:{"type":"iteration","mode":"review","run":1,"status":"complete","focus":"correctness audit of the continuity handoff into the default Stage 3 MMR path","dimensions":["correctness"],"filesReviewed":[".opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.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/intent-classifier.ts",".opencode/skills/system-spec-kit/shared/algorithms/adaptive-fusion.ts",".opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts"],"sessionId":"2026-04-13T11:05:00Z-001-search-fusion-tuning-review","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":1,"findingsSummary":{"P0":0,"P1":1,"P2":0},"findingsNew":{"P0":0,"P1":1,"P2":0},"newFindingsRatio":0.55,"findingRefs":["F001"],"timestamp":"2026-04-13T11:18:00Z","durationMs":54000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-state.jsonl:4:{"type":"iteration","mode":"review","run":2,"status":"complete","focus":"correctness and security sweep of telemetry, rerank minimum, save routing, and live config flags","dimensions":["correctness","security"],"filesReviewed":[".opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts",".opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts",".mcp.json",".claude/mcp.json",".vscode/mcp.json",".gemini/settings.json","opencode.json"],"sessionId":"2026-04-13T11:05:00Z-001-search-fusion-tuning-review","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":1,"findingsSummary":{"P0":0,"P1":1,"P2":0},"findingsNew":{"P0":0,"P1":0,"P2":0},"newFindingsRatio":0.0,"findingRefs":["F001"],"timestamp":"2026-04-13T11:31:00Z","durationMs":46000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-state.jsonl:5:{"type":"iteration","mode":"review","run":3,"status":"complete","focus":"traceability audit of requested search docs versus the live Stage 3 continuity branch","dimensions":["traceability","maintainability"],"filesReviewed":[".opencode/commands/memory/search.md",".opencode/skills/system-spec-kit/ARCHITECTURE.md",".opencode/skills/system-spec-kit/mcp_server/configs/README.md","README.md",".opencode/skills/system-spec-kit/SKILL.md",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts"],"sessionId":"2026-04-13T11:05:00Z-001-search-fusion-tuning-review","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":2,"findingsSummary":{"P0":0,"P1":2,"P2":0},"findingsNew":{"P0":0,"P1":1,"P2":0},"newFindingsRatio":0.42,"findingRefs":["F001","F002"],"timestamp":"2026-04-13T11:46:00Z","durationMs":51000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-state.jsonl:7:{"type":"iteration","mode":"review","run":4,"status":"complete","focus":"traceability follow-up across feature catalog retrieval docs and supporting summaries","dimensions":["traceability"],"filesReviewed":[".opencode/skills/system-spec-kit/feature_catalog/feature_catalog.md",".opencode/skills/system-spec-kit/feature_catalog/01--retrieval/02-semantic-and-lexical-search-memorysearch.md",".opencode/skills/system-spec-kit/feature_catalog/01--retrieval/05-4-stage-pipeline-architecture.md",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts"],"sessionId":"2026-04-13T11:05:00Z-001-search-fusion-tuning-review","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":2,"findingsSummary":{"P0":0,"P1":2,"P2":0},"findingsNew":{"P0":0,"P1":0,"P2":0},"newFindingsRatio":0.0,"findingRefs":["F002"],"timestamp":"2026-04-13T11:58:00Z","durationMs":33000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-state.jsonl:8:{"type":"iteration","mode":"review","run":5,"status":"complete","focus":"cross-reference audit of phase 005 packet evidence versus the live continuity code path","dimensions":["traceability"],"filesReviewed":[".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/005-doc-surface-alignment/spec.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/005-doc-surface-alignment/tasks.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/005-doc-surface-alignment/implementation-summary.md",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts"],"sessionId":"2026-04-13T11:05:00Z-001-search-fusion-tuning-review","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":3,"findingsSummary":{"P0":0,"P1":3,"P2":0},"findingsNew":{"P0":0,"P1":1,"P2":0},"newFindingsRatio":0.38,"findingRefs":["F002","F003"],"timestamp":"2026-04-13T12:12:00Z","durationMs":43000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-state.jsonl:10:{"type":"iteration","mode":"review","run":6,"status":"complete","focus":"traceability and maintainability review of child checklist closure across phases 001-004","dimensions":["traceability","maintainability"],"filesReviewed":[".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/001-remove-length-penalty/checklist.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/003-continuity-search-profile/checklist.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/001-remove-length-penalty/tasks.md",".opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-continuity-research/001-search-fusion-tuning/004-raise-rerank-minimum/tasks.md"],"sessionId":"2026-04-13T11:05:00Z-001-search-fusion-tuning-review","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":4,"findingsSummary":{"P0":0,"P1":4,"P2":0},"findingsNew":{"P0":0,"P1":1,"P2":0},"newFindingsRatio":0.36,"findingRefs":["F003","F004"],"timestamp":"2026-04-13T12:27:00Z","durationMs":47000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-state.jsonl:16:{"type":"iteration","mode":"review","run":9,"status":"complete","focus":"stabilization pass across live configs, non-Codex mirrors, and inspected playbook surfaces","dimensions":["traceability","maintainability"],"filesReviewed":[".mcp.json",".claude/mcp.json",".vscode/mcp.json",".gemini/settings.json","opencode.json",".gemini/agents/deep-review.md",".gemini/agents/context.md",".opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md"],"sessionId":"2026-04-13T11:05:00Z-001-search-fusion-tuning-review","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":6,"findingsSummary":{"P0":0,"P1":6,"P2":0},"findingsNew":{"P0":0,"P1":0,"P2":0},"newFindingsRatio":0.0,"findingRefs":["F005","F006"],"timestamp":"2026-04-13T13:09:00Z","durationMs":36000}
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./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/implementation-summary.md:123:3. **CocoIndex bootstrap timed out.** The synthesis relies on direct reads, reducer state, and source citations instead.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/legacy-memory-quarantine/12-03-26_18-50__governance.md:276:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance" })` |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/legacy-memory-quarantine/12-03-26_18-50__governance.md:288:memory_search({ specFolder: "system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance", limit: 10 })
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/legacy-memory-quarantine/12-03-26_18-50__governance.md:294:memory_search({ query: "orphaned", anchors: ["state"] })
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/legacy-memory-quarantine/12-03-26_18-50__governance.md:303:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/legacy-memory-quarantine/12-03-26_18-50__governance.md:495:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/legacy-memory-quarantine/12-03-26_18-50__governance.md:496:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/issue-registry.md:40:| P0-004 | Column mismatch: last_accessed vs last_accessed_at | 042 | VERIFIED_OPEN | vector-index.js:2241 uses `last_accessed_at` but schema has `last_accessed` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/issue-registry.md:65:| P1-012 | Embedding loss during checkpoint restore | 042 | VERIFIED_OPEN | checkpoints.js sets status='pending', embeddings not preserved |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/issue-registry.md:100:| P3-003 | sqlite-vec status not visible in responses | 031 | VERIFIED_OPEN | Users can't see if vector extension loaded |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/issue-registry.md:102:| P3-005 | Embedding status not shown to users | 031 | VERIFIED_OPEN | No indication of embedding generation state |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/issue-registry.md:252:8. Add embedding backup to checkpoints (P1-012)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/004-graphify/graph-metadata.json:205:    "causal_summary": "Phase 4 of `001-research-graph-context-systems` is a read-only audit of the graphify external Python skill to translate its two-pass codebase knowledge graph patterns 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 grounded in specific `external/graphify/` file:line citations, not a generic feature inventory. No source files outside this spec folder are modified during the research phase.",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:52:- [x] CHK-003 [P1] Dependencies identified and available [E:plan.md:186-194 Section 6 DEPENDENCIES - SQLite FTS5 (Green), Embedding API/Local (Green), Cross-encoder (Yellow/optional), BM25-WASM (Green with JS fallback)]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:54:- [x] CHK-005 [P1] Feature flag strategy defined with env variables [E:plan.md:543-567 L3+ FEATURE FLAG STRATEGY - Phase 1: SPECKIT_SESSION_DEDUP/LAZY_LOAD, Phase 2: SPECKIT_RRF/BM25/USAGE/TYPE_DECAY, Phase 3: SPECKIT_RELATIONS/CROSS_ENCODER/NO_LEGACY, migration path documented]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:55:- [x] CHK-006 [P2] Open questions Q1-Q8 resolved or defaults documented [E:spec.md:390-402 Section 16 OPEN QUESTIONS - Q1-Q8 all have recommended defaults: Q1=file path+frontmatter, Q2=k=60, Q3=Voyage rerank-2, Q4=automatic+override, Q5=2+ occurrences, Q6=SQLite, Q7=existing files, Q8=test drift defaults]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:96:- [x] CHK-021 [P0] Deferred initialization pattern implemented (Lazy Singleton) [E:shared/embeddings.js]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:103:- [x] CHK-025 [P0] `RECOVERY_HINTS` catalog covers memory_search, checkpoint_restore, memory_save
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:134:  - [E:code] Already exists in schema: `access_count INTEGER DEFAULT 0` (vector-index.js:831)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:142:  - [E:code] Exists as `last_accessed INTEGER DEFAULT 0` (vector-index.js:832)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:165:- [x] CHK-041 [P1] Vector, BM25, and optional Graph sources combined
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:166:  - [E:code] lib/search/rrf-fusion.js:28-32 - SOURCE_TYPES={VECTOR,BM25,GRAPH}
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:181:### BM25 Hybrid Search (P1)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:183:- [x] CHK-045 [P1] BM25 search integrated with FTS5 [E:lib/search/hybrid-search.js:combined_lexical_search() - merges FTS5+BM25]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:184:- [x] CHK-046 [P1] BM25-WASM or JS fallback implementation [E:lib/search/bm25-index.js - pure JS (no WASM package exists), k1=1.2, b=0.75]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:185:- [x] CHK-047 [P2] Keyword retrieval complements vector search [E:lib/search/hybrid-search.js:hybrid_search_enhanced() - use_bm25 option]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:189:- [x] CHK-048 [P1] Optional reranking via `options.rerank` parameter
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:191:  - [E:code] rerank() function accepts query and documents array
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:227:  - [E:code] formatters/search-results.js uses envelope for memory_search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:240:- [x] CHK-062 [P1] Indexes on source_id and target_id for performance (R5 mitigation) [E:vector-index.js migration v8 - idx_causal_source, idx_causal_target, idx_causal_relation, idx_causal_strength]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:271:  - [E:code] memory_context tool in L1 serves as unified entry point, progressively discloses to L2-L7
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:290:- [x] CHK-138 [P1] ACRONYM_MAP populated with technical terms (e.g., "RRF", "FSRS", "BM25") - ACRONYM_MAP in fuzzy-match.js:44-115 with 50+ terms
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:330:  - [E:code] incremental-index.js:156-167 - content_unchanged path avoids embedding regeneration
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:340:  - [E:code] lib/validation/preflight.js:check_duplicate() with exact (SHA-256 hash) + similar (vector) detection
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:374:  - [E:code] lib/embeddings/provider-chain.js:743 uses getRecoveryHint() for E052 errors
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:377:  - [E:code] lib/ organized into 17 domain modules: architecture, cache, cognitive, config, embeddings, errors, interfaces, learning, parsing, providers, response, scoring, search, session, storage, utils, validation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:381:  - [E:code] lib/interfaces/ contains only 3 files: index.js, vector-store.js, embedding-provider.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:382:  - [E:code] IVectorStore interface in vector-store.js for database abstraction (line 60)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:383:  - [E:code] IEmbeddingProvider interface in embedding-provider.js for embedding abstraction
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:441:  - [E:code] shared/embeddings/factory.js:27 process.env.VOYAGE_API_KEY
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:442:  - [E:code] shared/embeddings/factory.js:34 process.env.OPENAI_API_KEY
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:452:  - [E:code] shared/embeddings.js implements lazy singleton pattern - provider not initialized until first use
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:481:  - [E:code] lib/search/vector-index.js - sqlite-vec extension with HNSW index for O(log n) vector search at scale
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:508:  - [E:code] lib/interfaces/vector-store.js: IVectorStore class with search/upsert/delete/get/getStats/isAvailable/close methods
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:509:  - [E:code] lib/interfaces/vector-store.js: MockVectorStore for testing (CHK-144)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:510:  - [E:code] lib/interfaces/embedding-provider.js: IEmbeddingProvider class with embed/batchEmbed/embedQuery/embedDocument/validateCredentials methods
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:511:  - [E:code] lib/interfaces/embedding-provider.js: MockEmbeddingProvider for testing (CHK-144)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:525:  - [E:code] vector-index.js:656-672 - Migrations wrapped in transaction with atomic rollback on failure
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:529:  - [E:code] bm25-index.js:42 - ENABLE_BM25 (default true)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:536:  - [E:code] vector-index.js:387-653 - v4 to v9 migrations (FSRS, memory_type, mtime, embedding_status, causal_edges, corrections)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:559:  - External API calls limited to: embedding providers (Voyage, OpenAI, Cohere) and reranking APIs
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:580:  - No PII transmitted to external services (only query embeddings sent to API providers)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:584:  - No telemetry, analytics, or external data transmission beyond embedding API calls
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:599:  - [E:code] Affected tools: memory_search, memory_match_triggers, memory_list_folders, memory_read
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:608:  - [E:code] lib/search/vector-index.js:581-585 - Migration v8 creates indexes:
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:618:- [x] CHK-161 [P1] R9 (Embedding provider): Fallback to BM25-only, IEmbeddingProvider interface
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:619:  - [E:code] lib/embeddings/provider-chain.js:62-148 - BM25OnlyProvider class implements partial IEmbeddingProvider
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:620:  - [E:code] lib/embeddings/provider-chain.js:160-161 - Fallback order: Primary API -> Local -> BM25-only (CHK-171)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:621:  - [E:code] lib/interfaces/embedding-provider.js:42-212 - IEmbeddingProvider interface with embed(), batchEmbed(), validateCredentials(), etc.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:658:- [x] CHK-167 [P0] API key validation occurs at MCP startup (not first use) [E:context-server.js:316-352 - called in main() before embedding warmup]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:665:- [x] CHK-171 [P0] Fallback order implemented: Primary API → Local (nomic-embed-text) → BM25-only [E:provider-chain.test.js:28 tests passing]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:673:- [x] CHK-176 [P0] Memory file created even when embedding fails [E:memory-save.js:499-543 indexMemoryDeferred path]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:674:- [x] CHK-177 [P0] `embedding_status` column used: 'complete', 'pending', 'partial', 'failed' [E:vector-index.js v7 migration with 'partial' status, CHECK constraint]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:675:- [x] CHK-178 [P0] Memories with `embedding_status: 'pending'` searchable via BM25/FTS5 [E:hybrid-search.js:193-196 FTS5 includes all memories regardless of embedding_status]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:676:- [x] CHK-179 [P1] Background retry job processes pending embeddings [E:retry-manager.js start_background_job() with 5min interval, opportunistic via memory-save.js:823-827]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:677:- [x] CHK-180 [P1] `memory_save` response includes `embedding_status` field [E:memory-save.js:792-801 response.embedding_status]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:697:- [x] CHK-191 [P0] Zero memory saves blocked by embedding failures (deferred indexing)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:698:  - [E:code] handlers/memory-save.js:532-549 - Embedding generation wrapped in try/catch, sets embedding_status='pending' on failure
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:699:  - [E:code] handlers/memory-save.js:692-741 - indexMemoryDeferred path creates memory without embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:700:  - [E:code] handlers/memory-save.js:746-762 - BM25 indexing ensures searchability even without embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:701:  - [E:code] CHK-176-CHK-180 prerequisites verified: files saved with 'pending' status, searchable via BM25/FTS5
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:702:- [x] CHK-192 [P1] 95% of pending embeddings completed within 24 hours
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:710:  - [E:code] lib/embeddings/provider-chain.js:601-613 - getFallbackLog() returns array of fallback events
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:711:  - [E:code] lib/embeddings/provider-chain.js:619-648 - getStatus() includes fallbackCount, lastFallback, provider activation info
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/checklist.md:712:  - [E:code] lib/embeddings/provider-chain.js:669-686 - _logFallback() records tier, provider, reason, timestamp
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-dashboard.md:49:| 2 | correctness and security sweep of telemetry, rerank minimum, save routing, and live config flags | correctness/security | 0.00 | 0/1/0 | complete |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-016.md:70:When `memory_search` returns empty or near-empty results (fewer than N fresh spec_doc hits), the search widens the filter to include archived memories:
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/review/deep-review-dashboard.md:47:| 12 | D5 Performance — vector and CLI retest | 1 | D5 Performance | 0/0/0 | 0.00 | complete |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/reaudit-2026-03-23/codex53-verifier.md:43:  - [vector-index-schema.ts#L1078](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L1078)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/reaudit-2026-03-23/codex53-verifier.md:49:  - `ensureGovernanceTables(database): void` exists ([vector-index-schema.ts#L1078](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L1078)).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/reaudit-2026-03-23/codex53-verifier.md:52:  - `retention_policy` default `'keep'` in schema/migration ([scope-governance.ts#L234](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/governance/scope-governance.ts#L234), [vector-index-schema.ts#L1063](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L1063)).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-findings-registry.json:18:      "file": ".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-findings-registry.json:20:      "description": "`handleMemorySearch()` maps `profile === 'resume'` to `adaptiveFusionIntent = 'continuity'`, and Stage 1 forwards that internal intent into hybrid search, but Stage 3 still selects its lambda from `config.detectedIntent`. Because `SPECKIT_MMR` defaults to enabled, resume-oriented searches can lose the continuity profile in the final ordering step. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:830`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:538`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:641`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:69`]",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-findings-registry.json:40:      "description": "the command contract, architecture doc, config README, repo README, and feature-catalog summaries now all say the final Stage 3 MMR pass uses continuity lambda `0.65`, but Stage 3 still selects lambda from `config.detectedIntent` rather than the internal continuity handoff used earlier in the pipeline. [SOURCE: `.opencode/commands/memory/search.md:102`] [SOURCE: `.opencode/skills/system-spec-kit/ARCHITECTURE.md:150`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/configs/README.md:49`] [SOURCE: `README.md:393`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-findings-registry.json:60:      "description": "the packet spec, tasks, checklist, and implementation summary all say the continuity Stage 3 MMR lambda behavior was verified and documented, but the runtime Stage 3 branch under review still ignores `adaptiveFusionIntent` and does not execute that continuity-aware handoff. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/spec.md:62`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/tasks.md:58`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:65`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/implementation-summary.md:61`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-findings-registry.json:80:      "description": "each of the first four child packets still carries `status: planned` plus unchecked items, so the `001` tree is not actually fully checklist-verified even though runtime work shipped and phase `005` is strict-clean. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:15`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md:15`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/003-continuity-search-profile/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/003-continuity-search-profile/checklist.md:13`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md:13`]",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-036.md:225:- keep a SQLite snapshot of archived rows plus a manifest of `row_id`, `source_path`, checksum, and embedding/index version
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-036.md:230:3. rebuild FTS/vector entries for the archived subset if required
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:51:No systematic review has been performed across the full runtime surface. Logic errors in causal graph traversal, transaction boundaries that do not cover file-system writes, race conditions in embedding generation, and edge cases in the chunking/thinning pipeline may exist undetected.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:69:| 2 | **Transaction safety** | `lib/storage/transaction-manager.ts`, `vector-index-mutations.ts` |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:71:| 4 | **Hybrid search pipeline** | `lib/search/hybrid-search.ts`, `bm25-index.ts`, `sqlite-fts.ts`, `vector-index-queries.ts` |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:72:| 5 | **Embedding lifecycle** | `lib/providers/embeddings.ts`, `lib/cache/embedding-cache.ts`, `vector-index-store.ts` |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:75:| 8 | **Schema migrations** | `lib/search/vector-index-schema.ts`, migration safety |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:104:- `lib/providers/*.ts` (embeddings, retry)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:167:| Dependency | CocoIndex semantic search for code discovery | Required for concept-based exploration | Verify CocoIndex MCP is available before starting |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:201:- Files with 2,000+ LOC (memory-save.ts, hybrid-search.ts, vector-index-schema.ts): review in focused slices.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/spec.md:205:- If CocoIndex is unavailable: fall back to Grep/Glob for code discovery.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:143:| Active File | .opencode/.../lib/vector-index.js |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:182:- `.opencode/.../lib/vector-index.js` - Entry point / exports
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:223:Comprehensive analysis and remediation of the Spec Kit & Memory system. First, 10 parallel Opus agents analyzed all 42 spec folders (035-042 active, 001-034 archived) to identify issues. Code verification agents confirmed which bugs still existed. After deduplication, 39 unique verified open issues were identified across P0 (8 critical), P1 (14 high), P2 (12 medium), and P3 (5 low) priorities. Then, 10 parallel Opus agents implemented fixes for ALL issues. Key fixes included: removing duplicate getConstitutionalMemories function, fixing column name mismatches, adding database migrations, implementing proper LRU cache eviction, adding trigger cache invalidation, preserving embeddings in checkpoint restore, aligning gate numbering (Gate 3→4), standardizing terminology, and documenting architecture decisions. All 39 issues were resolved - 30 newly fixed, 9 already fixed.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:232:- Decision: Modified checkpoint create/restore to include vec_memories embeddings
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:241:| `.opencode/.../lib/vector-index.js` | Modified during session |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:264:Comprehensive analysis and remediation of the Spec Kit & Memory system. First, 10 parallel Opus agents analyzed all 42 spec folders (035-042 active, 001-034 archived) to identify issues. Code verification agents confirmed which bugs still existed. After deduplication, 39 unique verified open issues were identified across P0 (8 critical), P1 (14 high), P2 (12 medium), and P3 (5 low) priorities. Then, 10 parallel Opus agents implemented fixes for ALL issues. Key fixes included: removing duplicate getConstitutionalMemories function, fixing column name mismatches, adding database migrations, implementing proper LRU cache eviction, adding trigger cache invalidation, preserving embeddings in checkpoint restore, aligning gate numbering (Gate 3→4), standardizing terminology, and documenting architecture decisions. All 39 issues were resolved - 30 newly fixed, 9 already fixed.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:266:**Details:** post-merge refinement | spec kit memory | 39 issues fixed | P0 P1 P2 P3 bugs | getConstitutionalMemories duplicate | last_accessed column | LRU cache eviction | trigger cache invalidation | checkpoint embeddings | gate numbering Gate 4 | terminology standardization | implementation-summary optional | 10 opus agents | 42 spec folders analyzed | vector-index.js fixes
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:440:### Decision 6: Decision: Modified checkpoint create/restore to include vec_memories embeddings because users expected checkpoint restore to preserve semantic search capability
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:442:**Context**: Decision: Modified checkpoint create/restore to include vec_memories embeddings because users expected checkpoint restore to preserve semantic search capability
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:451:   Decision: Modified checkpoint create/restore to include vec_memories embeddings because users expected checkpoint restore to preserve semantic search capability
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:457:**Rationale**: Decision: Modified checkpoint create/restore to include vec_memories embeddings because users expected checkpoint restore to preserve semantic search capability
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:601:Comprehensive analysis and remediation of the Spec Kit & Memory system. First, 10 parallel Opus agents analyzed all 42 spec folders (035-042 active, 001-034 archived) to identify issues. Code verification agents confirmed which bugs still existed. After deduplication, 39 unique verified open issues were identified across P0 (8 critical), P1 (14 high), P2 (12 medium), and P3 (5 low) priorities. Then, 10 parallel Opus agents implemented fixes for ALL issues. Key fixes included: removing duplicate getConstitutionalMemories function, fixing column name mismatches, adding database migrations, implementing proper LRU cache eviction, adding trigger cache invalidation, preserving embeddings in checkpoint restore, aligning gate numbering (Gate 3→4), standardizing terminology, and documenting architecture decisions. All 39 issues were resolved - 30 newly fixed, 9 already fixed.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:622:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/043-post-merge-refinement-final" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:627:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:740:  - ".opencode/.../lib/vector-index.js"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:762:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/scratch/legacy-memory-quarantine/26-12-25_08-12__post-merge-refinement-final.md:763:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/deep-research-dashboard.md:141:- **Live MCP handler calls** — embedding warmup timeout blocked live retrieval tests (same failure as phase 017 generation 1 and 2); deferred to phase 019
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/deep-research-dashboard.md:154:1. **Phase 018 Gate A pre-work** — run root packet backfill + embedding health check + SQLite backup
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:23:- Re-litigating already shipped length-penalty, telemetry, or rerank-threshold behavior unless the live code contradicts the packet claims.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:67:### `SKILL.md` drift on this exact point: the skill-level search summary is broad about continuity, rerank gating, and telemetry, but it does not explicitly promise the continuity Stage 3 lambda is already active. [SOURCE: `.opencode/skills/system-spec-kit/SKILL.md:592`] -- BLOCKED (iteration 3, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:68:- What was tried: `SKILL.md` drift on this exact point: the skill-level search summary is broad about continuity, rerank gating, and telemetry, but it does not explicitly promise the continuity Stage 3 lambda is already active. [SOURCE: `.opencode/skills/system-spec-kit/SKILL.md:592`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:70:- Do NOT retry: `SKILL.md` drift on this exact point: the skill-level search summary is broad about continuity, rerank gating, and telemetry, but it does not explicitly promise the continuity Stage 3 lambda is already active. [SOURCE: `.opencode/skills/system-spec-kit/SKILL.md:592`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:87:### Feature-catalog telemetry and neutral-length notes are stale: the reviewed catalog surfaces correctly describe rerank gating at four rows plus compatibility-only length scaling and telemetry counters. [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/01--retrieval/05-4-stage-pipeline-architecture.md:25`] [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/feature_catalog.md:241`] -- BLOCKED (iteration 4, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:88:- What was tried: Feature-catalog telemetry and neutral-length notes are stale: the reviewed catalog surfaces correctly describe rerank gating at four rows plus compatibility-only length scaling and telemetry counters. [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/01--retrieval/05-4-stage-pipeline-architecture.md:25`] [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/feature_catalog.md:241`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:90:- Do NOT retry: Feature-catalog telemetry and neutral-length notes are stale: the reviewed catalog surfaces correctly describe rerank gating at four rows plus compatibility-only length scaling and telemetry counters. [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/01--retrieval/05-4-stage-pipeline-architecture.md:25`] [SOURCE: `.opencode/skills/system-spec-kit/feature_catalog/feature_catalog.md:241`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:92:### Hidden late-cycle P0 across the reviewed runtime and doc surfaces: the final pass did not surface any data-loss, auth-bypass, or hard-gate defect beyond the already active P1 set. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`] -- BLOCKED (iteration 10, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:93:- What was tried: Hidden late-cycle P0 across the reviewed runtime and doc surfaces: the final pass did not surface any data-loss, auth-bypass, or hard-gate defect beyond the already active P1 set. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:95:- Do NOT retry: Hidden late-cycle P0 across the reviewed runtime and doc surfaces: the final pass did not surface any data-loss, auth-bypass, or hard-gate defect beyond the already active P1 set. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:137:### Phase 005 over-claimed the rerank gate or telemetry surfaces: those parts of the packet remain aligned with the live runtime. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:64`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:66`] -- BLOCKED (iteration 5, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:138:- What was tried: Phase 005 over-claimed the rerank gate or telemetry surfaces: those parts of the packet remain aligned with the live runtime. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:64`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:66`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:140:- Do NOT retry: Phase 005 over-claimed the rerank gate or telemetry surfaces: those parts of the packet remain aligned with the live runtime. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:64`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:66`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:142:### Playbook regression on the inspected reranker scenario: the updated manual-testing surface accurately describes telemetry counters and compatibility-only length scaling without repeating the continuity Stage 3 claim. [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:19`] [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:30`] -- BLOCKED (iteration 9, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:143:- What was tried: Playbook regression on the inspected reranker scenario: the updated manual-testing surface accurately describes telemetry counters and compatibility-only length scaling without repeating the continuity Stage 3 claim. [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:19`] [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:30`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:145:- Do NOT retry: Playbook regression on the inspected reranker scenario: the updated manual-testing surface accurately describes telemetry counters and compatibility-only length scaling without repeating the continuity Stage 3 claim. [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:19`] [SOURCE: `.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/098-local-gguf-reranker-via-node-llama-cpp-p1-5.md:30`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:152:### Rerank-threshold drift: Stage 3 still skips reranking below four rows and forwards the compatibility `applyLengthPenalty` flag without reintroducing length-based scoring. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:321`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:383`] -- BLOCKED (iteration 2, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:153:- What was tried: Rerank-threshold drift: Stage 3 still skips reranking below four rows and forwards the compatibility `applyLengthPenalty` flag without reintroducing length-based scoring. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:321`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:383`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:155:- Do NOT retry: Rerank-threshold drift: Stage 3 still skips reranking below four rows and forwards the compatibility `applyLengthPenalty` flag without reintroducing length-based scoring. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:321`] [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:383`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:162:### Searching for a hidden continuity-aware Stage 3 override did not surface any alternate path beyond `config.detectedIntent` and `INTENT_LAMBDA_MAP`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`] -- BLOCKED (iteration 1, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:163:- What was tried: Searching for a hidden continuity-aware Stage 3 override did not surface any alternate path beyond `config.detectedIntent` and `INTENT_LAMBDA_MAP`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:165:- Do NOT retry: Searching for a hidden continuity-aware Stage 3 override did not surface any alternate path beyond `config.detectedIntent` and `INTENT_LAMBDA_MAP`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:172:### Task-list incompleteness: the child `tasks.md` files are all marked `status: complete`; the closure gap is in checklist verification rather than implementation task execution. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/tasks.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/tasks.md:3`] -- BLOCKED (iteration 6, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:173:- What was tried: Task-list incompleteness: the child `tasks.md` files are all marked `status: complete`; the closure gap is in checklist verification rather than implementation task execution. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/tasks.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/tasks.md:3`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:175:- Do NOT retry: Task-list incompleteness: the child `tasks.md` files are all marked `status: complete`; the closure gap is in checklist verification rather than implementation task execution. [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/tasks.md:3`] [SOURCE: `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/tasks.md:3`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:210:- CocoIndex MCP calls were attempted during setup but returned cancelled-tool responses, so the review used direct file reads, grep sweeps, and validator runs.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:222:| `playbook_capability` | overlay | pass | 9 | The inspected reranker playbook surface accurately reflects telemetry and compatibility-only length-penalty behavior without repeating the continuity claim. |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:230:| `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts` | D1, D3, D4 | 10 | 0 P0, 2 P1, 0 P2 | complete |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:248:| `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md` | D3 | 6 | 0 P0, 1 P1, 0 P2 | complete |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/deep-review-strategy.md:250:| `.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md` | D3 | 6 | 0 P0, 1 P1, 0 P2 | complete |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:58:- **Files:** `.opencode/skills/system-spec-kit/mcp-server/src/context-server.js`, `vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:98:- **Files:** `.opencode/skills/system-spec-kit/mcp-server/src/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:99:- **Evidence:** vector-index.js:2241 uses `last_accessed_at` but schema has `last_accessed`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:119:- **Files:** `.opencode/skills/system-spec-kit/mcp-server/src/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:194:  4. [ ] Replace `memory_search` with `spec_kit_memory_memory_search`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:419:- **Files:** `.opencode/skills/system-spec-kit/mcp-server/src/vector-index.js` or cache module
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:440:- **Evidence:** checkpoints.js sets status='pending', embeddings not preserved
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:443:  2. [ ] Ensure embeddings are included in checkpoint data
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:445:  4. [ ] Preserve embedding data during restore
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:446:  5. [ ] Don't reset status to 'pending' if embeddings exist
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:448:  7. [ ] Verify embeddings preserved after restore
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:451:  - No need to regenerate embeddings after restore
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:505:- **Files:** `.opencode/skills/system-spec-kit/mcp-server/src/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:526:- **Files:** `.opencode/skills/system-spec-kit/mcp-server/src/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/tasks.md:686:  3. [ ] Add unit tests for vector-index.js core functions
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:51:- [x] Dependencies identified (CocoIndex MCP, repo DB)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:94:| 002 | Transaction safety | `lib/storage/transaction-manager.ts`, `vector-index-mutations.ts` |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:97:| 005 | Embedding lifecycle | `lib/providers/embeddings.ts`, `lib/cache/embedding-cache.ts` |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:100:| 008 | Schema migrations | `lib/search/vector-index-schema.ts` |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:123:- [ ] Verify CocoIndex MCP is available for semantic code search
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:156:- [ ] WS-2: Fix 3 high-impact search performance bottlenecks (S-1 fallback re-pipeline, S-2 token double-serialize, S-3 BM25 full scan) + 4 medium (S-4 degree N+1, S-5 graph FTS OR, S-6 fusion duplication, S-7 MMR re-fetch)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:158:- [ ] WS-4: Fix 1 high error recovery gap (E-1 chunked PE partial commit) + 3 medium (E-2 safe-swap cleanup, E-3 BM25 rollback drift, E-4 reconsolidation BM25 repair)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:171:| Read-only audit | Full mcp_server/ source tree | Grep, Glob, Read, CocoIndex |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/plan.md:183:| CocoIndex Code MCP | External | Green | Falls back to Grep/Glob for code discovery |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-002.md:88:When Tier 1 yields low confidence (<0.7), compute the embedding of the chunk and compare against prototype vectors for each category. Prototypes are 5-10 sample chunks per category captured during phase 018 design work and stored in `config/routing-prototypes.json`. Nearest-prototype classification with cosine similarity.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-002.md:90:Cost: one embedding per ambiguous chunk. Reuses the existing `generateOrCacheEmbedding` from `save/embedding-pipeline.ts`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-002.md:119:Unstructured input (raw markdown or free-form text) falls through to Tier 1 pattern matching → Tier 2 embedding → Tier 3 LLM.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-002.md:134:- **F2.3**: Tier 2 embedding similarity reuses the existing embedding pipeline (`save/embedding-pipeline.ts`). No new infrastructure needed.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-002.md:147:- The three-tier classification strategy (rule → embedding → LLM) bounds cost while preserving accuracy. Most chunks hit Tier 1.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-16__speckit-reimagined.md:399:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-16__speckit-reimagined.md:400:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/017-governance/scratch/reaudit-2026-03-23/gpt54-analyst.md:15:Evidence: the catalog claims are directly implemented: hierarchical scope model ([03-hierarchical-scope-governance-governed-ingest-retention-and-audit.md#L18](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/feature_catalog/17--governance/03-hierarchical-scope-governance-governed-ingest-retention-and-audit.md#L18), [scope-governance.ts#L21](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/governance/scope-governance.ts#L21), [scope-governance.ts#L449](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/governance/scope-governance.ts#L449)); required provenance on governed ingest ([03-hierarchical-scope-governance-governed-ingest-retention-and-audit.md#L20](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/feature_catalog/17--governance/03-hierarchical-scope-governance-governed-ingest-retention-and-audit.md#L20), [scope-governance.ts#L229](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/governance/scope-governance.ts#L229), [memory-save.ts#L630](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts#L630)); retention integration and delete auditing ([03-hierarchical-scope-governance-governed-ingest-retention-and-audit.md#L22](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/feature_catalog/17--governance/03-hierarchical-scope-governance-governed-ingest-retention-and-audit.md#L22), [retention.ts#L41](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/governance/retention.ts#L41), [retention.ts#L98](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/governance/retention.ts#L98)); audit schema/support and post-insert persistence ([vector-index-schema.ts#L1078](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L1078), [memory-save.ts#L815](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts#L815)). Tests cover the same behaviors ([memory-governance.vitest.ts#L23](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-governance.vitest.ts#L23), [memory-governance.vitest.ts#L130](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-governance.vitest.ts#L130), [memory-governance.vitest.ts#L235](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-governance.vitest.ts#L235)).  
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/review/deep-research-state.jsonl:13:{"type": "iteration", "mode": "review", "run": 12, "status": "complete", "focus": "D5 Performance \u2014 vector and CLI retest", "dimension": "5 Performance", "dimensions": ["D5 Performance"], "findingsCount": 0, "newFindingsRatio": 0.0, "noveltyJustification": "stabilization/adjudication pass", "findingsSummary": {"P0": 0, "P1": 0, "P2": 0}, "filesReviewed": [".opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement"], "dimensionScores": {"correctness": 2, "security": 2, "traceability": 2, "maintainability": 2}, "findingsNew": {"P0": 0, "P1": 0, "P2": 0}, "findingsRefined": {"P0": 0, "P1": 0, "P2": 0}, "upgrades": [], "resolved": [], "findingRefs": [], "traceabilityChecks": {"summary": {"required": 2, "executed": 2, "pass": 2, "partial": 0, "fail": 0, "blocked": 0, "notApplicable": 0, "gatingFailures": 0}, "results": []}, "coverage": {"filesReviewed": 1, "filesTotal": 1, "dimensionsComplete": []}, "ruledOut": ["The hot-path duplicate hashing advisory stands; no new higher-severity latency issue was confirmed in this pass."], "timestamp": "2026-04-02T18:32:00", "durationMs": 33000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:11:The review did not uncover a release-blocking P0, but it did confirm six active P1 issues spanning the live continuity rerank path, repo docs, packet-local verification evidence, Codex mirror accuracy, and packet-tree closure state. The most important runtime defect is still the Stage 3 continuity handoff: resume-style searches route `adaptiveFusionIntent = 'continuity'` into Stage 1, but the default MMR pass still reads `detectedIntent`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:23:- **F001 [P1 | correctness]** Stage 3 MMR ignores the internal continuity handoff. Evidence: [`.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:830`], [`.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:538`], [`.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`], [`.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts:641`], [`.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts:69`].
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:24:- **F002 [P1 | traceability]** Repo-level search docs now describe a continuity-aware Stage 3 lambda that the runtime does not execute. Evidence: [`.opencode/commands/memory/search.md:102`], [`.opencode/skills/system-spec-kit/ARCHITECTURE.md:150`], [`.opencode/skills/system-spec-kit/mcp_server/configs/README.md:49`], [`README.md:393`], [`.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`].
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:25:- **F003 [P1 | traceability]** The `005-doc-surface-alignment` packet records the continuity Stage 3 lambda behavior as verified shipped reality even though the runtime path still ignores `adaptiveFusionIntent` in Stage 3. Evidence: [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/spec.md:62`], [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/tasks.md:58`], [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/checklist.md:65`], [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/005-doc-surface-alignment/implementation-summary.md:61`], [`.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209`].
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:26:- **F004 [P1 | traceability]** Child packets `001-004` are not fully verification-closed: each checklist still carries `status: planned` with unchecked items, so the `001` tree is not actually fully checklist-verified. Evidence: [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:3`], [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/001-remove-length-penalty/checklist.md:15`], [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/002-add-reranker-telemetry/checklist.md:3`], [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/003-continuity-search-profile/checklist.md:13`], [`.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/001-search-fusion-tuning/004-raise-rerank-minimum/checklist.md:13`].
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:64:| `playbook_capability` | overlay | pass | The inspected reranker playbook surface accurately reflects telemetry and neutral length-scaling behavior. |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:69:- `SKILL.md` is not part of the active drift set: it correctly mentions continuity profile, rerank gate, and telemetry without explicitly promising the Stage 3 continuity lambda is already live.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:70:- No new security-sensitive regressions were found in `memory-save.ts`, the live MCP configs, or the reranker telemetry path during this review.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:78:| 1-2 | Code correctness | Found F001; ruled out telemetry, rerank-gate, and Tier 3 config/runtime drift |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:90:| `002-add-reranker-telemetry/` | FAIL (`exit 2`, `Errors: 3`, `Warnings: 7`) |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/003-graph-metadata-validation-research/review-report.md:92:| `004-raise-rerank-minimum/` | FAIL (`exit 2`, `Errors: 4`, `Warnings: 6`) |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/deep-research-strategy.md:75:- Semantic bootstrap was unavailable because CocoIndex timed out. (iteration 1)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/deep-research-strategy.md:115:### CocoIndex semantic bootstrap timed out before producing usable hits, so iteration evidence came from direct reads and `rg`. -- BLOCKED (iteration 1, 1 attempts)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/deep-research-strategy.md:116:- What was tried: CocoIndex semantic bootstrap timed out before producing usable hits, so iteration evidence came from direct reads and `rg`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/deep-research-strategy.md:118:- Do NOT retry: CocoIndex semantic bootstrap timed out before producing usable hits, so iteration evidence came from direct reads and `rg`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/deep-research-strategy.md:204:- CocoIndex semantic bootstrap timed out before producing usable hits, so iteration evidence came from direct reads and `rg`. (iteration 1)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/deep-research-strategy.md:242:- CocoIndex bootstrap timed out after 120 seconds for both External Project external source and Public graph/memory/skill code; continue with `rg`, direct file reads, and sidecar read-only explorers.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/findings-registry.json:52:      "resolution": "contentRouter with 3-tier classifier (rule \u2192 embedding \u2192 LLM), 8 content categories, confidence tiers, refuse-to-route at <0.5",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/findings-registry.json:161:      "title": "3-tier classifier (rule \u2192 embedding \u2192 LLM) handles 80/15/5 split",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/research-findings.md:80:- Fixed split-brain `vector-index.js` versions
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-012.md:122:| 12. Embedding semantic search | 7 | no change |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-55__speckit-reimagined.md:278:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-55__speckit-reimagined.md:283:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-55__speckit-reimagined.md:377:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-55__speckit-reimagined.md:378:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/deep-research-state.jsonl:8:{"event":"iteration_complete","generation":1,"iteration":7,"band":"B","timestamp":"2026-04-11T14:05:00Z","scope":"q4_features_2_12_13","focus":"Intent routing + modes + 4-stage pipeline + embedding.","findings":5,"new_info_ratio":0.75,"stop_reason":"iteration_7_done","maps_to_questions":["Q4"],"output":"research/iterations/iteration-007.md"}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/deep-research-state.jsonl:27:{"event":"iteration_complete","generation":2,"iteration":21,"band":"E","timestamp":"2026-04-11T16:10:00Z","scope":"tier2_classifier_prototype","focus":"contentRouter Tier 2 embedding classifier prototype library","findings":5,"worker":"cli-codex gpt-5.4 high fast","lines":150,"output":"research/iterations/iteration-021.md"}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-026.md:108:- Recovery: stop before indexing or embedding; preserve input file content as-is; return concrete validation errors plus the bypass option; no DB or doc mutation occurs.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-026.md:165:- Detector: phase 018 semantic search still uses embeddings; mismatch is detected when stored embedding metadata no longer matches `embeddings.getModelName()` or dimension expectations, analogous to `embedding-pipeline.ts:128-170`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-026.md:166:- Recovery: keep lexical indexing and canonical docs live, mark semantic retrieval pending, enqueue a re-embedding pass, and return partial-service hints instead of blocking the save.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-026.md:167:- User text: `Embedding model changed; lexical indexing completed, but re-embedding is required for semantic search.`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-026.md:168:- Log entry: `[embedding-pipeline] code=SI003 action=defer_reembed model=current!=stored file=implementation-summary.md`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-026.md:169:- Repro: change the configured embedding model or vector dimension, then resume against rows generated under the old model.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:53:| P0-001 | Duplicate getConstitutionalMemories | vector-index.js | Wrapper pattern: internal at L209, public at L1199 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:56:| P0-004 | Column name mismatch | vector-index.js | All `last_accessed_at` → `last_accessed` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:57:| P0-005 | related_memories column missing | vector-index.js | Migration at L459-467 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:71:| P1-006 | LRU cache access time | vector-index.js | accessTime tracking at L2354-2379 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:77:| P1-012 | Checkpoint embeddings | checkpoints.js | Preserved at L64-93 (create), L386-422 (restore) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:85:| P2-001 | Database indexes | vector-index.js | 3 indexes at L538-567 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:86:| P2-002 | Timestamp format docs | vector-index.js | Comment at L518-529 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:115:| `mcp_server/lib/vector-index.js` | P0-001, P0-004, P0-005, P1-006, P2-001, P2-002 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:160:| Agent 1 | vector-index.js | P0-001, P0-004, P0-005, P1-006, P2-001, P2-002 | ✅ 6/6 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:212:1. **MCP Server Restart** - Required to apply changes to vector-index.js and context-server.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/043-post-merge-refinement-final/implementation-summary.md:213:2. **Functional Testing** - Run memory_search, checkpoint_create/restore after restart
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-034.md:122:- Several other direct mutation surfaces bypass the `causal-edges.ts` helper. From prior audit knowledge: `vector-index-mutations.ts` deletes causal edges during memory removal, `corrections.ts` deletes correction-owned edges, and `graph-lifecycle.ts` updates edge strengths — none of those paths call `clearGraphSignalsCache()`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-034.md:213:1. `graph-signals.ts:54-57` — Cache invalidation incomplete: direct `causal_edges` writers (vector-index-mutations, corrections, graph-lifecycle) bypass `clearGraphSignalsCache()`, causing stale momentum/depth scores in ranking until an unrelated session boundary.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/spec.md:79:| `mcp_server/lib/search/vector-index-schema.ts` | Modify | Enforce canonical context type values in schema |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-22__speckit-reimagined.md:317:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-22__speckit-reimagined.md:322:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-22__speckit-reimagined.md:416:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-22__speckit-reimagined.md:417:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-010.md:8:- `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/plan.md:36:| **Storage** | SQLite vector index + migration tooling |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-010.md:34:**Issue**: `normalizeMarkdownLists()` removes both unchecked (`- [ ]`) and checked (`- [x]` / `- [X]`) prefixes, so pending and completed tasks normalize to identical text. In this codebase that is not just a retrieval-quality tradeoff: the normalized text is used for embedding cache keys and chunk cache keys, so flipping a task from incomplete to complete can reuse the same normalized hash and stale embedding even though the task state changed.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-010.md:39:- Normalized content is used to compute embedding cache keys at [`embedding-pipeline.ts:114-116`](../../../../../../skill/system-spec-kit/mcp_server/handlers/save/embedding-pipeline.ts#L114) and chunk cache keys at [`chunking-orchestrator.ts:89-90`](../../../../../../skill/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts#L89).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-010.md:40:- The same normalized text also feeds BM25 document text at [`bm25-index.ts:305-309`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/bm25-index.ts#L305), and tasks/checklists are explicitly indexed as spec documents at [`memory-parser.ts:252-258`](../../../../../../skill/system-spec-kit/mcp_server/lib/parsing/memory-parser.ts#L252) and [`memory-parser.ts:693-700`](../../../../../../skill/system-spec-kit/mcp_server/lib/parsing/memory-parser.ts#L693).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:42:  - Call memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:44:  - Vector channel: embedding compute (~50ms if cache hit, ~500ms+ if cold)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:45:  - BM25 channel: SQLite FTS query (~20ms)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:48:  - RRF fusion + rerank (~50ms)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:111:- No embedding compute on the happy path
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:124:| RRF fusion + rerank | 50ms | 0ms | **-50ms** |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:171:| Embedding cold cache | 30s timeout then error | Not touched (no embedding compute) |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-013.md:180:- **F13.1**: Resume latency drops from ~1200ms to ~300ms (4x improvement) by skipping embedding compute + SQL queries on the happy path.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:6:  missing memory commands, embedding resilience documentation, and Gate 3 alignment
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:12:- embedding resilience documentation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:131:- [ ] Create embedding_resilience.md reference file (REQ-029-033)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:198:- **All embedding resilience features (REQ-029-033) undocumented**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:302:| `memory/` | 4 | 40% | 8 gaps, needs embedding_resilience.md |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:340:- `memory/embedding_resilience.md` (new file)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:372:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:384:memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined", limit: 10 })
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:390:memory_search({ query: "orphaned", anchors: ["state"] })
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:399:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:542:  - "embedding-resilience"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:562:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-53__speckit-reimagined.md:563:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-004.md:8:- `002-add-reranker-telemetry/decision-record.md`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-004.md:10:- `004-raise-rerank-minimum/decision-record.md`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-004.md:11:- `004-raise-rerank-minimum/implementation-summary.md`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-004.md:16:| DRV-P1-004 | P1 | Child decision records in phases 001-004 still declare `status: planned` even though the corresponding packet surfaces are closed and shipped. | [SOURCE: 001-remove-length-penalty/decision-record.md:1-3]; [SOURCE: 002-add-reranker-telemetry/decision-record.md:1-3]; [SOURCE: 003-continuity-search-profile/decision-record.md:1-3]; [SOURCE: 004-raise-rerank-minimum/decision-record.md:1-3]; [SOURCE: 004-raise-rerank-minimum/implementation-summary.md:1-11] |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/001-cache-warning-hooks/spec.md:97:- Any attempt to make cached summaries or hook metadata authoritative over `session_bootstrap()` or `memory_context(...resume...)`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/001-cache-warning-hooks/spec.md:130:| REQ-006 | This packet must preserve startup authority boundaries. | No doc or code path in this packet claims cached summary or Stop metadata replaces `session_bootstrap()` or `memory_context({ input: "resume previous work", mode: "resume", profile: "resume" })` [SOURCE: research.md §4]. |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/001-cache-warning-hooks/spec.md:171:- **Authority preservation**: `session_bootstrap()` and `memory_context(...resume...)` remain authoritative.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-024.md:8:**Issue** `memory_context` documents `focused` as the intent-optimized path, but explicit `mode: "focused"` requests do not classify intent unless the caller also supplies `intent`. `resolveEffectiveMode()` only runs the classifier inside the `requestedMode === "auto"` branch, and `executeFocusedStrategy()` then forces `autoDetectIntent: false` when delegating to `memory_search`. The same query therefore gets intent-aware ranking in `auto -> focused`, but loses that optimization in explicit `focused`, producing inconsistent results for the same logical retrieval path.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-024.md:12:**Fix** When `effectiveMode === "focused"` and no explicit intent was provided, either classify intent before calling `executeFocusedStrategy()` or pass `autoDetectIntent: true` through to `memory_search`. That keeps explicit `focused` behavior aligned with the auto-routed focused lane.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-024.md:35:**Issue** The strategy helpers blindly spread the `MCPResponse` returned by `memory_search` / `memory_match_triggers` into `ContextResult`, and the main handler only converts thrown exceptions into `E_STRATEGY`. If a downstream handler returns a normal MCP error envelope (`isError: true`) instead of throwing, `memory_context` still emits a success summary like "Context retrieved via focused mode", with the real error buried inside nested `content[0].text`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/iterations/iteration-001.md:36:- CocoIndex semantic bootstrap timed out before producing usable hits, so iteration evidence came from direct reads and `rg`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/iterations/iteration-001.md:50:- What did not work and why: Semantic bootstrap was unavailable because CocoIndex timed out.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/iterations/iteration-001.md:51:- What I would do differently: Start future runs by indexing the external tree only after confirming CocoIndex health.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/agent-16-feature-catalog.md:4:- Updated `feature_catalog/FEATURE_CATALOG.md` summary lines for `memory_context`, RSF shadow mode, and local GGUF reranker behavior.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/agent-16-feature-catalog.md:5:- Corrected `memory_context` session semantics to reflect caller-scoped reuse: cross-turn dedup and resume context require a caller-supplied `sessionId`; anonymous calls receive an ephemeral UUID for that invocation only.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/agent-16-feature-catalog.md:7:- Corrected local reranker activation details to match current gate logic: strict `RERANKER_LOCAL=true`, rollout-gated enablement, readable model file, and total-memory thresholds of 8GB default / 2GB with custom model path.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/agent-16-feature-catalog.md:8:- Corrected local reranker fallback wording to match implementation: when the local path cannot run or fails, it returns the incoming order unchanged rather than introducing a separate RSF/RRF fallback step.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:44:| Read (`memory_context` / `memory_search`) | 160-190ms | 285ms | 380-430ms | Meets the `<300ms` search target only if gather stays parallel |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:61:| Index sync (`atomicIndexMemory`, FTS/vector/ledger) | 360ms | 220ms | 520ms | Yes | Possibly async later, but not for phase 018 | Instrument in `handlers/memory-save.ts` before/after index mutation + `save/response-builder.ts` completion |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:82:| Lexical gather (FTS5/BM25) | 45ms | 20ms | 65ms | No, unless it overtakes vector | Yes | Emit `lexical_gather_ms` from stage 1 gather |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:84:| Fusion + rerank | 55ms | 35ms | 80ms | Yes | No | Instrument in `stage2-fusion.ts` and `stage3-rerank.ts` |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:91:- The vector branch is the dominant gather branch. If it rises above ~110ms at p95, search will miss target even if every other stage is healthy.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:92:- Fusion/rerank is the main serial post-gather cost. It is the right place to look if search feels slower without any single channel being obviously bad.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:136:- Read: add `read_path_ms`, `read.stage.intent_ms`, `read.stage.trigger_probe_ms`, `read.stage.vector_ms`, `read.stage.lexical_ms`, `read.stage.graph_ms`, `read.stage.fusion_ms`, `read.stage.filter_ms`, `read.stage.materialize_ms`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-027.md:177:- **F27.4**: Stage-level budget burn is the right dashboard primitive. End-to-end p95 alone is too coarse to tell whether the regression came from lock wait, vector gather, rerank, or fallback ladder churn.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-53__speckit-reimagined.md:336:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/z_archive/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-53__speckit-reimagined.md:341:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-53__speckit-reimagined.md:452:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_11-53__speckit-reimagined.md:453:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-005.md:7:- `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-005.md:9:- `.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-005.md:16:- The continuity lambda handoff, rerank threshold, and no-op length-penalty behavior all match the child packet claims reviewed so far.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:5:### [P1] Hybrid fallback thresholds use fractional values, but vector search interprets them as percentages
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:8:`.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:11:The fallback pipeline passes `minSimilarity` values like `0.3`, `0.17`, and `0.1` into the vector channel as if they were 30%, 17%, and 10%. The vector layer does not treat them that way: it divides `minSimilarity` by 100 before converting to a cosine-distance cutoff. That means Tier 1 is effectively using a 0.3% similarity floor, so vector retrieval is almost unfiltered and the Tier 1 -> Tier 2 widening barely changes the vector candidate set.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:14:`hybridSearchEnhanced()` forwards `options.minSimilarity` directly into `vectorSearchFn(...)` at `.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:865-870`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:16:`vector_search()` converts that option with `2 * (1 - minSimilarity / 100)` at `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:197`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:17:The same file uses whole-number defaults like `30` and `50` in the enriched vector entry points at `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:708` and `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:795`, which confirms the vector contract is percentage-based, not fractional.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:20:Pick one contract and enforce it everywhere. The smallest fix is to change the hybrid fallback constants to `30`, `17`, and `10`. If the intended contract is 0-1 floats, then convert inside `hybrid-search.ts` before calling the vector layer and update the vector-search API/docs accordingly.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:31:`collectRawCandidates()` falls back to unconditional FTS and BM25 calls at `.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:1476-1485`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:48:There is no matching `options.useGraph === false` guard or `activeChannels.delete('degree')` alongside the vector/BM25/FTS disable logic at `.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts:820-823`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:53:### [P2] FTS query sanitization preserves punctuation that the BM25 tokenizer splits, so path/code queries lose FTS recall
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:59:The BM25 tokenizer and the FTS query sanitizer normalize queries differently. BM25 replaces most punctuation with spaces before tokenization, but the FTS path preserves characters like `.`, `/`, and `-`, then wraps the whole token in quotes. Queries that look like file paths or symbol-like identifiers can therefore split cleanly for BM25 while staying as a single quoted token for FTS, which makes the lexical channels disagree on what the user asked for.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:62:`tokenize()` in `.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:135-141` lowercases input and replaces `[^a-z0-9\\s-_]` with spaces, so `memory_search.ts` becomes BM25 terms roughly equivalent to `memory_search` and `ts`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-004.md:65:So a query like `memory_search.ts` is normalized one way for BM25 and another way for FTS, which distorts the lexical fusion inputs for code-like/path-like searches.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:2:title: "Iteration 007 — Intent routing, memory_context modes, 4-stage search pipeline retarget (Features 2, 12, 13)"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:9:focus: "Retarget intent-aware retrieval + modes + embedding search + RRF fusion."
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:26:- **Feature 2**: Intent-aware retrieval (`memory_context` modes + 7 intent types)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:27:- **Feature 12**: Embedding-based semantic search (Voyage 1024-dim)
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:34:- `memory_context` (L1 orchestration, `handlers/memory-context.ts:1610 LOC`) routes queries to `memory_search` or `memory_match_triggers` based on intent
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:37:- `memory_search` runs the 4-stage pipeline: gather → score → rerank → filter
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:38:- RRF (Reciprocal Rank Fusion) combines results from: vector channel, bm25 channel, fts5 channel, graph channel, trigger channel
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:39:- Voyage embeddings at 1024 dimensions
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:51:All four channels (vector, bm25, fts5, graph) operate on whichever document_types the query targets. The RRF fusion logic is unchanged.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:58:| `quick` | Top-K only, no rerank | Same; deprioritize archived (weight × 0.3) |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-007.md:61:| `resume` | `memory_context({ mode: "resume" })` | **NEW**: bypasses SQL entirely, reads `_memory.continuity` directly from the packet's handover.md + implementation-summary.md. Falls through to SQL only if neither doc exists. |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_10-53__speckit-reimagined.md:289:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_10-53__speckit-reimagined.md:294:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_10-53__speckit-reimagined.md:388:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_10-53__speckit-reimagined.md:389:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-001.md:10:- `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-001.md:18:- No direct correctness defect was confirmed in the shipped Stage 3 rerank implementation during this pass.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-010.md:100:- **Evidence Check**: Both wrappers now resolve their targets with `import.meta.dirname` (`mcp_server/scripts/map-ground-truth-ids.ts:10`, `mcp_server/scripts/reindex-embeddings.ts:9`), so the crash condition identified in iteration 008 is gone.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:26:`handlers/checkpoints.ts:393-407` rebuilds BM25 and clears search + constitutional caches, but does not call either `clearDegreeCacheForDb()` or `invalidateHierarchyCache()`. `handlers/mutation-hooks.ts:19-103` clears trigger, tool, constitutional, graph-signals, and co-activation caches only. The omitted caches are stateful: `lib/search/graph-search-fn.ts:309-318` and `lib/search/graph-search-fn.ts:479-509` keep per-DB degree scores until manually cleared, and `lib/search/spec-folder-hierarchy.ts:35-44` keeps a per-DB hierarchy cache behind a manual invalidator. A usage sweep found `invalidateHierarchyCache()` only in tests, not in production code. `lib/search/graph-search-fn.ts:90-105` shows that graph search does consume hierarchy rows during spec-scoped retrieval.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:31:### [P2] The vector-index layer still contains a live import cycle across query, mutation, and cache helpers
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:33:`mcp_server/lib/search/vector-index-aliases.ts`, `mcp_server/lib/search/vector-index-queries.ts`, `mcp_server/lib/search/vector-index-mutations.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:36:There is a real circular dependency in the core vector-index surface: aliases import queries, queries import mutations, and mutations import aliases. It happens to work today because the cycle mostly traverses function exports, but this makes initialization order brittle and raises the risk of partially initialized exports if any leg adds new module-scope work.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:39:`lib/search/vector-index-aliases.ts:13-23` imports query helpers from `vector-index-queries`. `lib/search/vector-index-queries.ts:21-32` imports `delete_memory_from_database` from `vector-index-mutations`. `lib/search/vector-index-mutations.ts:13-15` imports `clear_search_cache` from `vector-index-aliases`. An import-graph sweep across the reviewed handler/search/storage files found this as the only strongly connected component.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:42:Break the cycle by extracting cache invalidation into a neutral module, for example `vector-index-cache.ts`, or by inverting the dependency so mutation code does not import the alias layer.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:46:`mcp_server/handlers/index.ts`, `mcp_server/context-server.ts`, `mcp_server/lib/search/vector-index-store.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-030.md:52:`context-server.ts:31-35` imports from `./handlers`. `handlers/index.ts:5-18` eagerly imports all handler modules before re-exporting them. One of the deeper transitive side effects is in `lib/search/vector-index-store.ts:47-67`, which synchronously reads `search-weights.json` and fixes `search_weights` at module load time.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/prompts/C10.md:103:  - `specs/system-spec-kit/022-hybrid-rag-fusion/feature_catalog/20--feature-flag-reference/05-5-embedding-and-api.md`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-033.md:59:5. `phase` is the stable step or artifact. Example: `handover_read`, `fingerprint`, `vector`, `ledger`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-033.md:74:| `read.stage.vector_ms` | `search.gather.vector` |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-033.md:112:| `index.sync.vector` | index | write: vector sync | `spec_folder,result_kind` | `doc_path` | always | MED | `mcp_server/handlers/memory-save.ts` | B/C |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-033.md:123:| `search.gather.vector` | search | read: vector candidate generation | `spec_folder,result_kind,is_archived` | `query_class` | rate 1/100 | MED | `mcp_server/lib/search/pipeline/stage1-candidate-gen.ts` | D |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-033.md:127:| `search.rank.rerank` | search | read: rerank | `spec_folder,result_kind,is_archived` | `query_class` | rate 1/100 | MED | `mcp_server/lib/search/pipeline/stage3-rerank.ts` | D |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-033.md:165:Subsystem note: the writer path is intentionally more verbose than the reader path because gate C and gate E close on safety, not just latency; search splits vector, lexical, graph, fusion, rerank, and filter because iteration 027 concluded that end-to-end p95 alone is too coarse; shadow spans stay separate because they are migration evidence, not steady-state latency source-of-truth.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:120:- **W-R (Search/Retrieval)**: BM25 hybrid search (T028-T031), intent-aware retrieval (T036-T039), cross-encoder reranking (T048-T051), fuzzy matching (T076-T078)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:123:- **W-I (Infrastructure)**: Recovery hints (T009-T011), response envelope (T040-T042), 7-layer architecture (T060-T063), embedding resilience (T087-T107), new commands (T118-T122)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:153:This was a Level 3+ spec (complexity 85/100) transforming SpecKit from basic context storage to an intelligent self-improving memory system. Implementation used parallel agent delegation pattern with standardized response envelopes and embedding fallback chains.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:159:2. Search/retrieval (BM25 hybrid, cross-encoder reranking)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:162:5. Infrastructure (7-layer architecture, embedding resilience)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:184:- `lib/search/bm25-index.js` - BM25 hybrid search implementation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:283:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:446:embedding_model: "voyage-3-lite"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_14-15__speckit-reimagined-complete.md:447:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/iterations/iteration-003.md:19:- Public `code_graph_context` already accepts CocoIndex/manual/graph seeds and emits LLM-oriented neighborhoods, which is a good foundation for External Project-style richer context. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/context.ts:166]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-006.md:4:Repeat the security review against the shared reranker and routing surfaces after the packet-level findings list stabilized.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/checklist.md:122:- [x] CHK-133: Fixed memory_drift_context → memory_context
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/checklist.md:263:| embedding_resilience.md | ✅ Clean | 0 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/checklist.md:265:| epistemic-vectors.md | ✅ Clean | 0 |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-020.md:12:**Fix** Move DB access to call-time `vectorIndex.getDb()` lookups, or extend `db-state` so every module with a retained DB handle or scheduler closure participates in rebind. For timer-based modules, stop and restart the job on rebind so it captures the fresh handle.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-020.md:17:**Issue** Retrieval session state is stored in a process-global singleton keyed only by raw `sessionId`. `memory_search` mutates and consumes that state directly from the request without validating that the caller actually owns the session. In a shared MCP process, one caller can accidentally or intentionally reuse another caller's `sessionId` and influence future dedup/goal-boost behavior.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/prompts/G1.md:73:  - `specs/system-spec-kit/022-hybrid-rag-fusion/feature_catalog/14--pipeline-architecture/19-embedding-retry-orchestrator.md`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:174:Comprehensive system-spec-kit folder reorganization using 10 parallel opus agents for analysis. Identified and fixed: 3 critical package.json path errors, 4 misplaced files (shared/utils.js, lib/errors.js, lib/channel.js, decision-format.md), 2 fragile shell script paths (archive.sh, common.sh), and 2 dead code references (rerank.py). All relocations used re-export wrappers for backward compatibility.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:177:- Fixed 3 critical package.json path errors (test:cli, test:embeddings, main entry)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:180:- Documented 2 dead code references (rerank.py) with explanatory comments
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:222:**Choice:** Add explanatory comments about non-existent rerank.py instead of removing reranker code
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:223:**Rationale:** The code has graceful fallback behavior (returns original results if reranker unavailable). Removing would risk breaking future implementations.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:224:**Alternatives Considered:** Remove all reranker code (destructive), Create stub rerank.py (maintenance burden)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:267:  - Task 7: Added comments about non-existent rerank.py
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:289:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:301:memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined", limit: 10 })
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:307:memory_search({ query: "orphaned", anchors: ["state"] })
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:316:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:484:  - "mcp_server/lib/search/reranker.js"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:499:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/02-02-26_17-45__speckit-reimagined.md:500:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-002.md:8:- `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/iterations/iteration-002.md:15:- Provider resolution is environment-gated and falls back cleanly when no reranker is configured.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:8:**Issue**: The merge path archives the old row and inserts a raw replacement row, but it never updates `active_memory_projection`, never runs the normal post-insert/indexing hooks, and the bridge reports the archived row ID back to the caller instead of the new merged row ID. Since vector retrieval joins through `active_memory_projection` and excludes archived rows, the merged survivor can disappear from search immediately after a successful merge.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:12:- Vector search only returns rows that both join through `active_memory_projection` and are not archived by default at [`vector-index-queries.ts:223-265`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts#L223).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:13:- The canonical mutation path explicitly upserts `active_memory_projection` on insert/update at [`vector-index-mutations.ts:85-101`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts#L85) and [`vector-index-mutations.ts:198-229`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts#L198), but the merge path bypasses it entirely.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:17:**Fix**: Make merge use the same append-only creation path as normal saves so the new record gets projection state, metadata, BM25/history updates, and the correct returned ID. At minimum, the merge transaction must upsert `active_memory_projection`, apply post-insert metadata, refresh interference/BM25 state, and have the bridge return `reconResult.newMemoryId` instead of the archived predecessor ID.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:20:**File**: `.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts`, `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts`, and `.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:22:**Issue**: The bridge stores conflict candidates through `vectorIndex.indexMemory()` without `appendOnly: true`. On a same-path save, `indexMemory()` updates the existing row instead of creating a new version. That makes `storedId === topMatch.id`, so reconsolidation drops into the legacy `executeConflict()` fallback that overwrites the existing row in place and skips the `supersedes` edge. Because `memory-save` returns early for reconsolidation hits, the normal append-only lineage path never runs.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:25:- The bridge conflict store path calls `vectorIndex.indexMemory()` with the incoming `filePath` and no append-only override at [`reconsolidation-bridge.ts:216-230`](../../../../../../skill/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts#L216).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:26:- `index_memory()` updates an existing row whenever the same folder/path key already exists unless `appendOnly` is set at [`vector-index-mutations.ts:169-194`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts#L169).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:28:- The no-distinct-ID branch of `executeConflict()` overwrites `content_text`, `title`, `content_hash`, and embedding in place and creates no `supersedes` edge at [`reconsolidation.ts:377-396`](../../../../../../skill/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts#L377).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:41:- The assistive path performs its own raw `vectorSearch()` and never applies the same scope filter before selecting `topId` at [`reconsolidation-bridge.ts:331-351`](../../../../../../skill/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts#L331).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:48:**File**: `.opencode/skills/system-spec-kit/mcp_server/lib/scoring/interference-scoring.ts` and `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:55:- Folder-wide refresh writes scores for every parent row in the folder, again without excluding retired memories, at [`vector-index-store.ts:563-578`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L563).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-014.md:56:- The retrieval path excludes archived rows and, by default, excludes deprecated tiers while only considering active projections at [`vector-index-queries.ts:223-265`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts#L223).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-017.md:65:| vec_memories embedding mismatch | Version mismatch | "Embedding model changed; re-embedding required" | Run reindex-embeddings script |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_12-19__speckit-reimagined.md:558:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "003-memory-and-spec-kit/082-speckit-reimagined" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_12-19__speckit-reimagined.md:563:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_12-19__speckit-reimagined.md:672:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/legacy-memory-quarantine/01-02-26_12-19__speckit-reimagined.md:673:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-001.md:16:- **Evidence**: `normalizeContextType()` now maps `decision -> planning` unconditionally (`scripts/lib/frontmatter-migration.ts:831-840`), and existing frontmatter values are normalized before `inferContextType()` runs (`scripts/lib/frontmatter-migration.ts:1095-1097`). Because `inferContextType()` preserves any existing non-`decision` value unchanged (`scripts/lib/frontmatter-migration.ts:1031-1046`), an explicit existing `decision` context on a memory file is silently rewritten to `planning`. That is not just a legacy-doc cleanup: downstream code still treats `decision` as a legitimate persisted value in schema and behavior (`mcp_server/lib/search/vector-index-schema.ts:2254`, `mcp_server/lib/validation/save-quality-gate.ts:340-352`, `scripts/core/memory-metadata.ts:72-78`).
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/scratch/legacy-memory-quarantine/03-02-25_00-00__verification-complete.md:323:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "** 083-memory-command-consolidation" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/scratch/legacy-memory-quarantine/03-02-25_00-00__verification-complete.md:328:2. **Load memory context** - Use memory_search to surface prior work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/scratch/legacy-memory-quarantine/03-02-25_00-00__verification-complete.md:439:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/scratch/legacy-memory-quarantine/03-02-25_00-00__verification-complete.md:440:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:5:### [P0] `get_embedding_dim()` can size the vector index for the wrong provider
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:6:**File**: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:8:**Issue**: `get_embedding_dim()` does not use the canonical provider-resolution rules before the provider is initialized. It returns `1024` whenever `VOYAGE_API_KEY` is merely present and `1536` whenever `OPENAI_API_KEY` is present, even if `EMBEDDINGS_PROVIDER=hf-local` explicitly forces the local 768-dim provider or if the Voyage key is a placeholder that the shared factory intentionally ignores. Because `initialize_db()` passes this helper into schema creation and dimension validation, a valid configuration can bootstrap the database with the wrong vector width and only fail later when real embeddings are generated.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:11:- [`vector-index-store.ts:88`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L88) returns dimensions from raw env presence checks instead of canonical provider resolution.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:12:- [`vector-index-store.ts:598`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L598) and [`vector-index-store.ts:662`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L662) use that helper during DB initialization/schema setup.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:13:- [`shared/embeddings/factory.ts:206`](../../../../../../skill/system-spec-kit/shared/embeddings/factory.ts#L206) resolves providers with different precedence: explicit `EMBEDDINGS_PROVIDER` first, then non-placeholder Voyage, then non-placeholder OpenAI, then `hf-local`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:14:- [`tests/embeddings.vitest.ts:46`](../../../../../../skill/system-spec-kit/mcp_server/tests/embeddings.vitest.ts#L46) and [`tests/embeddings.vitest.ts:66`](../../../../../../skill/system-spec-kit/mcp_server/tests/embeddings.vitest.ts#L66) explicitly codify those canonical rules.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:16:**Fix**: Replace the ad hoc env checks in `get_embedding_dim()` with the same startup-resolution path used by the shared embeddings package, so dimension selection is derived from the resolved provider/model profile rather than raw key presence.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:18:### [P1] Provider-specific database isolation is bypassed before the embedding provider initializes
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:19:**File**: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:21:**Issue**: `resolve_database_path()` only uses `profile.getDatabasePath()` when `getEmbeddingProfile()` already has a live provider instance. The shared embeddings facade returns `null` until lazy initialization completes, so first-touch callers open the generic `DEFAULT_DB_PATH` instead of a provider/model/dimension-specific database. That defeats the intended isolation between 768-, 1024-, and 1536-dim indexes and turns provider switches into shared-DB integrity failures.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:24:- [`vector-index-store.ts:206`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L206) falls back to `DEFAULT_DB_PATH` when no profile is available.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:25:- [`shared/embeddings.ts:735`](../../../../../../skill/system-spec-kit/shared/embeddings.ts#L735) returns `null` from `getEmbeddingProfile()` until `providerInstance` exists.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:26:- [`retry-manager.ts:441`](../../../../../../skill/system-spec-kit/mcp_server/lib/providers/retry-manager.ts#L441) and many store entry points call into `initializeDb()/getDb()` before any embedding call has initialized the provider.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:31:### [P1] The SQLite embedding cache can replay stale vectors after a dimension change
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:32:**File**: `.opencode/skills/system-spec-kit/mcp_server/lib/cache/embedding-cache.ts`, `.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:34:**Issue**: Cache rows store `dimensions`, but `lookupEmbedding()` ignores that field and keys lookups only by `(content_hash, model_id)`. In `retryEmbedding()`, a cache hit is rehydrated directly into a `Float32Array` and treated as authoritative without checking the stored dimension against the current embedding dimension. If the same model name is reused with a different configured dimension, the retry path can serve a stale cached vector and attempt to persist it into the current index.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:37:- [`embedding-cache.ts:38`](../../../../../../skill/system-spec-kit/mcp_server/lib/cache/embedding-cache.ts#L38) stores `dimensions` alongside each cached embedding.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:38:- [`embedding-cache.ts:67`](../../../../../../skill/system-spec-kit/mcp_server/lib/cache/embedding-cache.ts#L67) reads `dimensions` but discards it and returns only the raw buffer.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:39:- [`retry-manager.ts:586`](../../../../../../skill/system-spec-kit/mcp_server/lib/providers/retry-manager.ts#L586) computes the cache key from normalized content plus `getModelName()`, then [`retry-manager.ts:592`](../../../../../../skill/system-spec-kit/mcp_server/lib/providers/retry-manager.ts#L592) rebuilds the vector from byte length alone.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:40:- [`shared/embeddings/factory.ts:143`](../../../../../../skill/system-spec-kit/shared/embeddings/factory.ts#L143) allows provider dimensions to vary independently of model names via explicit `dim` overrides, so `model_id` is not a sufficient cache discriminator.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-005.md:42:**Fix**: Include the resolved embedding dimension in the cache key and/or return the cached dimension from `lookupEmbedding()` so the retry path can reject and evict stale entries before reuse.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-038.md:81:Excluded on purpose: raw chunk text, user IDs, query text, provider error strings, embeddings, and whole-doc fingerprints.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-038.md:256:6. routing prototype embedding cache is invalidated and regenerated
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-038.md:306:| embedding every whole-doc diff | expensive and hard to interpret on naturally evolving docs | confirmed fingerprint library keyed by chunk hash |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/iterations/iteration-009.md:20:- Defer: LadybugDB storage migration, embeddings, web UI parity, and generated AI skills until Public has measured bottlenecks or concrete UX need.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/tasks.md:195:- ✅ Fixed `memory_drift_context` → `memory_context` (everywhere)
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:13:- File: `mcp_server/handlers/memory-index.ts`, `mcp_server/handlers/save/dedup.ts`, `mcp_server/handlers/memory-save.ts`, `mcp_server/handlers/save/create-record.ts`, `mcp_server/lib/search/vector-index-mutations.ts`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:14:- Line: `memory-index.ts:367-406`, `dedup.ts:182-239`, `242-307`, `memory-save.ts:728-805`, `927-981`, `create-record.ts:166-177`, `180-250`, `vector-index-mutations.ts:194-253`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:18:  - The save pipeline performs embedding-cache lookup / generation before the write transaction, and because the duplicate guards above are disabled under `force`, unchanged files still reach that stage. On a cache miss they will regenerate embeddings even though content is unchanged. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:728-805`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:19:  - The write path then enters an immediate transaction and, for same-path existing files, routes through append-only lineage logic. That ultimately forces `vector-index` into the `INSERT` path instead of the in-place `UPDATE` path when `appendOnly` is true. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts:927-981`; `.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:166-177`; `.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:180-250`; `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts:194-253`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:23:  - For a 1,201-file forced scan, unchanged files still pay parse/validate/cache-lookup costs, may pay provider embedding costs on cache miss, and still incur DB write churn. That makes runtime close to a full rewrite and explains the large dedup cleanup afterward.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:26:  - Move the cheapest unchanged test (mtime/content-hash/canonical-path) ahead of embedding generation and ahead of append-only lineage insertion, so unchanged files can be counted as revalidated without re-embedding and re-inserting.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:49:- Performance-wise, the table does have an index on `file_path`, so a one-off 14k-row dedup grouped by that column is not alarming on its own. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1929-1930`; `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2375`; `.opencode/skills/system-spec-kit/mcp_server/lib/storage/schema-downgrade.ts:178`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:55:- In the reviewed code, adding `'planning'` appears in table-creation / rebuild DDL, not as a standalone `ALTER TABLE ... ADD CONSTRAINT` on an existing SQLite table. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2254`; `.opencode/skills/system-spec-kit/mcp_server/lib/storage/schema-downgrade.ts:137`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-006.md:56:- The normal upgrade path shown in this file adds the `context_type` column without rebuilding the table, so this change does not introduce a new per-row validation sweep on already-upgraded databases. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1656-1659`]
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-031.md:48:| lib/storage/reconsolidation.ts | 856 | P0 (merge reachability, projection/lineage/BM25 upsert) |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-031.md:55:| lib/search/vector-index-store.ts | 1,087 | P0 (dimension guard), Sprint1 (concurrent DB switching) |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-031.md:56:| lib/search/vector-index-mutations.ts | 769 | Sprint1 (active projection fail-hard) |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-031.md:57:| lib/search/vector-index-schema.ts | 2,290 | Sprint2 (4 migration fixes: DDL, v12, v23, constitutional) |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-031.md:63:| lib/cache/embedding-cache.ts | 228 | Sprint2 (dimension-aware cache key) |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-031.md:91:| Highest-density files | hybrid-search.ts (2,247 LOC, 6 fixes), vector-index-schema.ts (2,290 LOC, 4 fixes), lineage-state.ts (1,418 LOC, 2 fixes) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/workflow-analysis-report.md:166:| ADR-002 | Hybrid BM25 | 3 options | Trade-off matrix |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/scratch/workflow-analysis-report.md:194:Primary (OpenAI) → Local Model → BM25-Only
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-state.jsonl:2:{"type":"iteration","mode":"review","run":1,"status":"complete","focus":"correctness - root packet closeout claim","dimensions":["correctness"],"filesReviewed":["spec.md","tasks.md","checklist.md",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts"],"sessionId":"rvw-2026-04-21T16-04-55Z","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":1,"findingsSummary":{"P0":0,"P1":1,"P2":0},"findingsNew":{"P0":0,"P1":1,"P2":0},"newFindingsRatio":1.0,"findingRefs":["DRV-P1-001"],"convergenceSignals":{"allDimensionsCovered":false,"p0Active":0,"churn":1.0,"decision":"continue"},"timestamp":"2026-04-21T16:08:55Z","durationMs":240000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-state.jsonl:4:{"type":"iteration","mode":"review","run":2,"status":"complete","focus":"security - code-path sweep","dimensions":["security"],"filesReviewed":[".opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts",".opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts"],"sessionId":"rvw-2026-04-21T16-04-55Z","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":1,"findingsSummary":{"P0":0,"P1":1,"P2":0},"findingsNew":{"P0":0,"P1":0,"P2":0},"newFindingsRatio":0.0,"findingRefs":[],"convergenceSignals":{"allDimensionsCovered":false,"p0Active":0,"churn":0.0,"decision":"continue"},"timestamp":"2026-04-21T16:11:55Z","durationMs":180000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-state.jsonl:8:{"type":"iteration","mode":"review","run":4,"status":"complete","focus":"maintainability - child ADR status hygiene","dimensions":["maintainability"],"filesReviewed":["001-remove-length-penalty/decision-record.md","002-add-reranker-telemetry/decision-record.md","003-continuity-search-profile/decision-record.md","004-raise-rerank-minimum/decision-record.md","004-raise-rerank-minimum/implementation-summary.md"],"sessionId":"rvw-2026-04-21T16-04-55Z","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":4,"findingsSummary":{"P0":0,"P1":4,"P2":0},"findingsNew":{"P0":0,"P1":1,"P2":0},"newFindingsRatio":0.25,"findingRefs":["DRV-P1-004"],"convergenceSignals":{"allDimensionsCovered":true,"p0Active":0,"churn":0.25,"decision":"continue"},"timestamp":"2026-04-21T16:19:55Z","durationMs":240000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-state.jsonl:10:{"type":"iteration","mode":"review","run":5,"status":"complete","focus":"correctness - re-read shipped code vs packet claims","dimensions":["correctness"],"filesReviewed":[".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts",".opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts",".opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts",".opencode/skills/system-spec-kit/mcp_server/tests/cross-encoder.vitest.ts"],"sessionId":"rvw-2026-04-21T16-04-55Z","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":4,"findingsSummary":{"P0":0,"P1":4,"P2":0},"findingsNew":{"P0":0,"P1":0,"P2":0},"newFindingsRatio":0.0,"findingRefs":[],"convergenceSignals":{"allDimensionsCovered":true,"p0Active":0,"churn":0.0,"decision":"continue"},"timestamp":"2026-04-21T16:23:55Z","durationMs":240000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-state.jsonl:20:{"type":"iteration","mode":"review","run":10,"status":"complete","focus":"security - final confirmation sweep","dimensions":["security"],"filesReviewed":[".opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts",".opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts",".opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts"],"sessionId":"rvw-2026-04-21T16-04-55Z","parentSessionId":null,"lineageMode":"new","generation":1,"continuedFromRun":null,"findingsCount":7,"findingsSummary":{"P0":0,"P1":7,"P2":0},"findingsNew":{"P0":0,"P1":0,"P2":0},"newFindingsRatio":0.0,"findingRefs":[],"convergenceSignals":{"allDimensionsCovered":true,"p0Active":0,"churn":0.0,"decision":"stop:maxIterationsReached"},"timestamp":"2026-04-21T16:44:55Z","durationMs":240000}
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/research.md:18:- Attempted a CocoIndex bootstrap, but semantic search timed out before usable hits. The final evidence therefore relies on direct `rg`, file reads, reducer state, and source citations.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/research.md:29:External Project also has a more agent-facing graph surface. `query` is concept-oriented and process-grouped, `context` provides callers/callees/references/process participation, and `impact` is framed as pre-change blast radius with depth groups, affected processes, modules, and risk levels [SOURCE: external/src/mcp/tools.ts:49] [SOURCE: external/src/mcp/tools.ts:172] [SOURCE: external/src/mcp/tools.ts:285]. Public's `code_graph_query` is currently relationship-operation oriented, while `code_graph_context` already accepts CocoIndex/manual/graph seeds and emits LLM-oriented neighborhoods [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/query.ts:20] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/context.ts:166]. The practical adaptation is to enrich Public's existing surfaces rather than replace them.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-028.md:76:- Sequence: audit blocker packets -> backfill canonical docs -> verify embedding health -> backup/restore DB -> rollback drill -> close.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-021.md:8:**Issue** `processPreparedMemory()` opens `BEGIN IMMEDIATE` before it awaits reconsolidation and file finalization. In the hot path, one save can hold both the in-process spec-folder mutex and the SQLite writer lock while it waits on embedding-backed reconsolidation or filesystem writes. That turns a per-folder serialization primitive into head-of-line blocking, and in multi-process callers it increases `SQLITE_BUSY` and lock inversion risk even when the actual row insert is short.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-021.md:10:**Evidence** `memory-save.ts:372-410` acquires the spec-folder lock and enters the save pipeline. `memory-save.ts:505-507` opens `BEGIN IMMEDIATE`, then `memory-save.ts:521-528` awaits `runReconsolidationIfEnabled(...)`, and `memory-save.ts:587-589` awaits `finalizeMemoryFileContent(...)` before `memory-save.ts:591` commits. The awaited reconsolidation helper is not purely local bookkeeping: `save/reconsolidation-bridge.ts:161-169,265-267` awaits `reconsolidate()` and lets that path generate embeddings inside the transaction window.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/implementation-summary.md:70:| `context.md` | Fixed MCP tool name `memory_drift_context` → `memory_context`; Updated deprecated refs; Fixed intent detection (phrase-based); Fixed date typo 2026→2025; Added emojis to 17 H2 sections |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/implementation-summary.md:83:| `mcp_server/README.md` | Fixed `memory_drift_context` → `memory_context`; Removed `memory_drift_learn`; Updated tool count 23→22 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/implementation-summary.md:111:| `memory_drift_context` | `memory_context` | context.md, mcp_server/README.md |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/implementation-summary.md:119:| L1 Orchestration | `memory_context` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/implementation-summary.md:120:| L2 Core | `memory_search`, `memory_match_triggers`, `memory_save` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/implementation-summary.md:184:1. **MCP Tool Names**: Use `memory_context` not `memory_drift_context`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/083-memory-command-consolidation/implementation-summary.md:278:- `memory_context` (replaces memory_drift_context)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:60:- [x] T004 [W-S][B:T001][B:T002] Integrate SessionManager into memory_search tool handler
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:72:  - Schema v5 migration in vector-index.js:437-494
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:96:  - ERROR_CODES constant: embedding (E001-E004), file (E010-E014), database (E020-E024),
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:100:  - TOOL_SPECIFIC_HINTS for contextual overrides (memory_search, checkpoint_restore, memory_save, etc.)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:127:- [x] T014 [W-I][B:T012] Integrate cache into memory_search with bypass option
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:136:  - Affected tools: memory_search, memory_match_triggers, memory_list_folders, memory_read
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:140:- [x] T016 [W-I] Refactor embedding provider to lazy singleton pattern (`shared/embeddings.js`)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:142:  - Added timing metrics: `provider_init_start_time`, `provider_init_complete_time`, `first_embedding_time`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:144:- [x] T017 [W-I][B:T016] Defer model initialization until first embedding request
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:151:- [x] T019 [W-I][B:T017] Update vector-index.js to use lazy provider
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:152:  - `get_embedding_dim()` now checks `isProviderInitialized()` before accessing profile
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:168:  - SOURCE_TYPES constant defines 'vector', 'bm25', 'graph' (lines 28-32)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:169:  - Each result includes sources[], source_count, and per-source flags (in_vector, in_fts, in_graph)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:170:  - Rank positions tracked (vector_rank, fts_rank, graph_rank) for debugging
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:175:- [x] T023 [W-R][B:T020] Create unified search entry point combining vector + BM25
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:177:  - Accepts sources: { vector, bm25, graph }
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:193:- [x] T027 [W-D][B:T024] Update memory_search to increment access_count
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:197:### Week 2-3: BM25 Hybrid Search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:199:- [x] T028 [W-R] Evaluate BM25-WASM vs pure JS implementation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:200:  - WASM: No BM25-WASM npm package exists (searched npm registry 2026-02-01)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:203:  - k1=1.2, b=0.75 (industry standard BM25 parameters)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:204:- [x] T029 [W-R][B:T028] Implement BM25Index class with fallback
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:205:  - Created `lib/search/bm25-index.js` with BM25Index class
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:208:  - ENABLE_BM25 feature flag (default: true)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:209:- [x] T030 [W-R][B:T029] Create BM25 document indexing on memory_index_scan
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:211:  - BM25 indexing added after vector indexing in index_memory_file()
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:213:  - Non-blocking: BM25 failures don't block memory save
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:214:- [x] T031 [W-R][B:T023][B:T029] Integrate BM25 results into RRF fusion
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:216:  - Added combined_lexical_search() merging FTS5 + BM25 results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:218:  - BM25 metadata added to search response for observability
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:258:- [x] T039 [W-R][B:T037] Add intent parameter to memory_search tool
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:259:  - Added `intent` parameter to memory_search tool schema (context-server.js:78)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:278:  - memory-triggers.js: 1 tool (memory_match_triggers)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:279:  - memory-search.js: 1 tool (memory_search) via format_search_results formatter
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:298:  - Added schema version 8 to vector-index.js run_migrations()
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:328:- [x] T048 [W-R][B:T031] Evaluate cross-encoder providers (Voyage rerank-2, Cohere, local models)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:330:  - Voyage rerank-2 (recommended for code/technical), Cohere rerank-v3.5, local cross-encoder/ms-marco-MiniLM-L-6-v2
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:334:  - `rerank_results()` main function with configurable providers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:343:  - Preserves raw score in `rerank_score_raw` field
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:344:- [x] T051 [W-R][B:T049] Integrate reranking as optional step (top-20 candidates)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:345:  - Added `rerank` and `applyLengthPenalty` params to memory_search handler
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:346:  - `apply_cross_encoder_reranking()` helper in memory-search.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:348:  - Integrated into multi-concept, hybrid, and vector search paths
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:353:- [x] T052 [W-G][B:T043] Create memory_corrections table schema - migration v9 in vector-index.js creates table with all required columns
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:362:- [x] T058 [W-D][B:T056] Add state filtering to memory_search - `filter_by_memory_state()` in memory-search.js + minState/applyStateLimits params
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:382:- [x] T061 [W-I][B:T060] Implement L1 Orchestration: memory_context unified entry
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:383:  - Created `handlers/memory-context.js` with handle_memory_context()
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:405:- [x] T065 [W-I][B:T064] Add shouldReindex() function - should_reindex() with mtime fast-path + content hash check + embedding status retry
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:422:  - `check_duplicate()` supports exact (content hash) and similar (vector) detection
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:430:  - Includes embedding API overhead in estimation (+150 tokens)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:470:  - 50+ technical acronyms: RRF, BM25, FSRS, LLM, MCP, ANCHOR, HOT/WARM/COLD, etc.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:473:- [x] T078 [W-R][B:T076] Add expandQueryWithFuzzy() to query expansion
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:508:- [x] T086 [W-I][B:T084] Refactor vector-index.js to implement interface
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:516:- [x] T087 [W-I] Implement `validateApiKey()` function in embedding provider factory
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:517:  - Implemented in `shared/embeddings/factory.js` lines 177-351
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:524:  - Called during main() startup before embedding model warmup
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:541:  - Created `lib/embeddings/provider-chain.js` with EmbeddingProviderChain class
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:542:  - Implements ordered fallback: Primary API -> Local -> BM25-only
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:544:- [x] T092 [W-I][B:T091] Add configurable primary embedding provider (default: Voyage)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:552:- [x] T094 [W-I][B:T091] Add BM25-only mode as tertiary fallback
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:553:  - BM25OnlyProvider class for text-only search mode
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:563:- [x] T096 [W-I] Add `embedding_status` column to memory_index schema (v4.2 migration)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:569:  - Deferred indexing path via `indexMemoryDeferred()` when embedding fails
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:570:  - PE gating only runs if embedding succeeded and candidates found
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:571:- [x] T098 [W-I][B:T096] Modify search to include `embedding_status: 'pending'` memories in BM25 results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:572:  - FTS5 search already includes all memories (no embedding_status filter)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:573:  - Only vector search filters by embedding_status='success'
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:575:- [x] T099 [W-I][B:T096] Implement background retry job for pending embeddings
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:579:- [x] T100 [W-I][B:T099] Add `embedding_status` to memory_save response envelope
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:580:  - Response includes embedding_status field (memory-save.js:792-801)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:582:  - Failure reason included when embedding fails
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:800:| T028-T031 | BM25 hybrid | T023 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tasks.md:802:| T048-T051 | Cross-encoder reranking | T031 |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-dashboard.md:31:| 002 | Code-path security sweep | `cross-encoder.ts`, `stage3-rerank.ts`, `content-router.ts` | security | `0/0/0` | `0.00` | complete |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-dashboard.md:34:| 005 | Correctness re-read of shipped code | `stage3-rerank.ts`, `cross-encoder.ts`, tests | correctness | `0/0/0` | `0.00` | complete |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-dashboard.md:39:| 010 | Final security confirmation | `cross-encoder.ts`, `stage3-rerank.ts`, `content-router.ts` | security | `0/0/0` | `0.00` | complete |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-015.md:26:Routing is driven only by complexity tier, not by intent or artifact class. As a result, very short spec/decision lookups are treated as simple queries and forcibly routed to `['vector', 'fts']`, which disables `bm25`, `graph`, and `degree` even when the query is really an exact artifact lookup or rationale lookup.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-015.md:29:The default simple-tier route is hardcoded to `['vector', 'fts']` at lines 57-61, and `routeQuery()` simply maps `classification.tier` to that subset at lines 121-139. The complexity classifier marks any query with `<= 3` terms as simple unless a longer-path condition applies in `.opencode/skills/system-spec-kit/mcp_server/lib/search/query-classifier.ts:172-182`. A direct probe of that classifier returned:
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-015.md:42:The classifier returns a single `intent` plus a flat keyword bag, so mixed queries lose facet-level intent structure. For cross-document questions that combine spec lookup and rationale lookup, only one intent survives and downstream fusion/reranking never sees the second retrieval objective.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-003.md:13:- File: `mcp_server/lib/search/vector-index-schema.ts`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-003.md:16:  - The upgrade path adds the column with `ALTER TABLE memory_index ADD COLUMN context_type TEXT DEFAULT 'general'` and does not attach a `CHECK` constraint. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1656-1659`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-003.md:17:  - Fresh schema creation does enforce `CHECK(context_type IN ('research', 'implementation', 'planning', 'general', 'decision', 'discovery'))`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2226-2255`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-003.md:42:- Reviewed `context_type` reads/writes are parameterized, e.g. `m.context_type = ?` in search queries and `context_type = ?` in update paths. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:247-249`; `.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts:503-514`; `.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts:215-229`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-018.md:93:1. Query reaches `memory_context(auto mode)`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:30:| Enhanced `getEmbeddingDim()` to check env vars | Provider might not be initialized when schema created | `vector-index.js:59-82` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:31:| Added `getEmbeddingProfileAsync()` function | Need async version that guarantees provider init | `embeddings.js:289-304` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:32:| Fixed `multiConceptSearch()` hardcoded dimension | Was using `EMBEDDING_DIM` instead of `getEmbeddingDim()` | `vector-index.js:1480-1487` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:33:| Fixed `memory_search()` hardcoded dimension | Was validating against hardcoded 768 instead of profile dimension | `context-server.js:674-679` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:40:| memory_search() dimension validation | RESOLVED | Fixed hardcoded 768 to use getEmbeddingProfile() |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:45:| `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js` | Enhanced getEmbeddingDim() to check env vars, fixed multiConceptSearch() | COMPLETE |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:46:| `.opencode/skills/system-spec-kit/scripts/lib/embeddings.js` | Added getEmbeddingProfileAsync() export | COMPLETE |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:55:- **Context:** All code fixes complete, need to verify memory_search() works after restart
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:59:2. Verify `memory_search()` works without dimension error
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:76:- [ ] Tests passing (if applicable) - PENDING: requires MCP restart for memory_search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:91:3. **Immediate cause #2**: `context-server.js:675` had hardcoded `if (queryEmbedding.length !== 768)` validation that rejected 1024-dimension Voyage embeddings. - **FIXED** (Session 2 / Attempt 1) by using `getEmbeddingProfile().dimension`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:101:| Verify memory_search() works | FAIL - found third bug |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/handover.md:113:memory_search({ query: "embedding dimension bug" })  // Should return results (not error)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:323:      embedding_status TEXT DEFAULT 'pending',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:360:    -- Vector embeddings (virtual table using sqlite-vec)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:362:    CREATE TABLE IF NOT EXISTS memory_embeddings (
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:364:      embedding BLOB,
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:372:    CREATE INDEX IF NOT EXISTS idx_memory_embedding_status ON memory_index(embedding_status);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:384:    DELETE FROM memory_embeddings;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:453:    (file_path, spec_folder, title, summary, stability, difficulty, last_review, review_count, importance_tier, embedding_status)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:506: * Mock embedding provider for testing without API calls
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:507: * Generates deterministic pseudo-embeddings based on content hash
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:515:     * Generate mock embedding for text
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:517:     * @returns {Promise<number[]>} Embedding vector
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:524:     * Batch generate embeddings
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:526:     * @returns {Promise<number[][]>} Array of embeddings
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:543: * Generate deterministic embedding from text (for reproducible tests)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:546: * @returns {number[]} Normalized embedding vector
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:549:  const embedding = new Array(dimensions);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:551:  // Simple hash-based pseudo-embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:561:    embedding[i] = (Math.sin(seed) + 1) / 2; // Normalize to [0, 1]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:564:  // Normalize to unit vector
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:565:  const magnitude = Math.sqrt(embedding.reduce((sum, v) => sum + v * v, 0));
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:566:  return embedding.map(v => v / magnitude);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:606:    model: 'text-embedding-3-small',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1002:    embeddingStatus: 'pending',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1086: * Create a configurable mock embedding provider
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1115:        throw new Error('Mock embedding generation failed');
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1118:      // Generate embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1125:      const embeddings = [];
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1127:        embeddings.push(await this.generateEmbedding(text));
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1129:      return embeddings;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1139:  const embedding = new Array(dimensions);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1141:    embedding[i] = Math.random() * 2 - 1;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1143:  const magnitude = Math.sqrt(embedding.reduce((sum, v) => sum + v * v, 0));
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1144:  return embedding.map(v => v / magnitude);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1405:          embedding_status TEXT DEFAULT 'pending',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1696:      memory_search: async (p) => {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1697:        // Simulate memory_search handler
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-implementation-guide.md:1764:      const searchResult = await callMcpTool('memory_search', {
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-009.md:67:Implementation: extend contamination gate to check the routing decision's confidence level. If the router returned confidence <0.7, the contamination gate runs an extra check comparing the content's embedding against the target anchor's prototype embeddings (from iteration 2's Tier 2 classifier prototypes).
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/decision-record.md:3:description: "The system has a hardcoded EMBEDDING_DIM = 768 constant in vector-index.js, but the active Voyage AI provider returns 1024-dimension embeddings. This causes 100% of memory index..."
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/decision-record.md:30:The system has a hardcoded `EMBEDDING_DIM = 768` constant in `vector-index.js`, but the active Voyage AI provider returns 1024-dimension embeddings. This causes 100% of memory indexing to fail.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/decision-record.md:36:| A) Dynamic lookup | Get dimension from embedding profile at runtime | Flexible, supports any provider | Slightly more complex |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/decision-record.md:150:When embedding provider dimension doesn't match database schema, should the system fail immediately or attempt partial indexing?
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/decision-record.md:183:| DR-001 | Dynamic embedding dimension | 2024-12-31 | Approved |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-007.md:38:- **No finding.** The active startup migration path wraps migrations in a single transaction before updating `schema_version` (`mcp_server/lib/search/vector-index-schema.ts:1152-1203`). The rename/copy downgrade path is also transaction-wrapped (`mcp_server/lib/storage/schema-downgrade.ts:268-304`). Under SQLite WAL semantics, readers should continue seeing the pre-transaction snapshot until commit rather than a half-migrated table layout.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-019.md:76:13. 4-stage pipeline — gather/score/rerank/filter all work
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:145:- Add performance tests measuring actual reranking latency
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:162:- BM25-only mode as tertiary fallback
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:164:- Fallback order verification (Primary -> Local -> BM25)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:170:- No tests for partial batch embedding failures
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:175:- Add tests for embedding dimension compatibility validation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:176:- Add stress tests for high-volume batch embedding
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:402:| **bm25-index.js** | lib/search/ | BM25 lexical search | HIGH - Fallback search |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:403:| **hybrid-search.js** | lib/search/ | Combines vector + BM25 | HIGH - Main search entry |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:414:| **vector-index.js** | lib/search/ | Vector embedding storage | HIGH - Core search |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:438:| **reranker.js** | lib/search/ | Reranking utilities | LOW - Wrapper |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:439:| **embeddings.js** | lib/providers/ | Embedding utilities | LOW - Wrapper |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:443:| **embedding-provider.js** | lib/interfaces/ | Provider interface | LOW - Abstract |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:444:| **vector-store.js** | lib/interfaces/ | Store interface | LOW - Abstract |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/existing-tests-audit.md:490:4. **Add tests for vector-index.js** - Core embedding storage
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:15:> **IMPORTANT:** The MCP server MUST be restarted before running memory/embedding tests. The dimension fix modifies `vector-index.js` but the MCP server caches code in memory. Without restart, `memory_index_scan()` will fail with the old dimension mismatch error.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:35:- `mcp_server/vector-index.js` (lines 59-70, 985, 1102)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:42:   grep -n "getEmbeddingDim" .opencode/skills/system-spec-kit/mcp_server/vector-index.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:48:   grep -n "getEmbeddingDim()" .opencode/skills/system-spec-kit/mcp_server/vector-index.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:54:   grep -n "Pre-flight embedding" .opencode/skills/system-spec-kit/mcp_server/context-server.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:210:2. **Verify test-embeddings-factory.js is documented:**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:212:   grep "test-embeddings-factory" .opencode/skills/system-spec-kit/SKILL.md
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:214:   **Expected:** Reference to test-embeddings-factory.js exists
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:218:- [ ] test-embeddings-factory.js referenced in SKILL.md
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:402:   memory_search({ query: "system analysis bugs" })
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:414:- [ ] memory_search() returns results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/testing-handover.md:458:- `mcp_server/vector-index.js`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-040.md:52:| `lib/providers/embeddings.ts` | YES |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/prompts/G2.md:60:  - `specs/system-spec-kit/022-hybrid-rag-fusion/feature_catalog/11--scoring-and-calibration/06-embedding-cache.md`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/prompts/G2.md:68:  - `specs/system-spec-kit/022-hybrid-rag-fusion/feature_catalog/11--scoring-and-calibration/14-local-gguf-reranker-via-node-llama-cpp.md`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-039.md:223:Fingerprint verification proves the canonical doc on disk matches the write plan. It does not prove the projection rows in `memory_index`, FTS, or vector state still match doc truth.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-039.md:249:- rebuild `memory_index`, FTS, and vector projections from that truth,
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/spec.md:31:**Embedding Dimension Mismatch** - The memory indexing system is broken because validation logic at `vector-index.js:967` uses a hardcoded 768-dimension constant while the active Voyage AI provider returns 1024-dimension embeddings. This causes 100% of memory file indexing to fail.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/spec.md:51:- Fix embedding dimension mismatch in vector-index.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/spec.md:69:1. Memory indexing works with any embedding provider (768, 1024, or other dimensions)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-coverage-matrix.md:162:### T028-T031: BM25 Hybrid Search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-coverage-matrix.md:166:| T028 | BM25 indexing | fuzzy-match.test.js | BM25 index tests | 5 | 3 | 2 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-coverage-matrix.md:173:**Status:** Partial - BM25 tests integrated with fuzzy match
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-coverage-matrix.md:457:| T093 | BM25-only mode | provider-chain.test.js | BM25 tests | 5 | 7 | 0 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/tests/test-coverage-matrix.md:622:2. **Overlap**: Some test files cover multiple task ranges where functionality is related (e.g., fuzzy-match.test.js covers both BM25 hybrid search and fuzzy matching).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-025.md:10:**Evidence** `trigger-matcher.ts:101-109` sets `MIN_PHRASE_LENGTH` to `3`. `trigger-matcher.ts:233-247` loads every 3+ character phrase into the trigger cache without any stop-word or semantic filtering, and `trigger-matcher.ts:466-484` tests all of them against the normalized prompt. The auto-surface hook calls this matcher directly on generic tool context in `hooks/memory-surface.ts:188-223`, so false positives are not limited to explicit `memory_match_triggers` calls. A denylist already exists for broad/noisy phrases in `lib/search/feedback-denylist.ts:5-6,60-82`, but this matcher never consults it.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-025.md:19:**Evidence** `trigger-matcher.ts:221-230` catches `JSON.parse()` failures and immediately `continue`s, and does the same for non-array payloads. There is already a shared tolerant parser in `lib/search/vector-index-types.ts:178-190`, but this code path bypasses it. Upstream trigger extraction accepts multiple frontmatter layouts in `lib/parsing/memory-parser.ts:464-528`, so malformed or shape-shifted metadata is a realistic failure mode rather than a purely theoretical one.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-025.md:21:**Fix** Replace the raw `JSON.parse()` branch with the shared `parse_trigger_phrases()` helper, and log invalid rows with at least `id` and `file_path`. Also expose an `invalidTriggerRows` counter in cache stats and surface a diagnostic hint from `memory_match_triggers` when rows were skipped, so broken frontmatter is observable instead of silent.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:47:- **Files:** `mcp_server/lib/parsing/memory-parser.ts`, `mcp_server/handlers/memory-save.ts`, `mcp_server/handlers/chunking-orchestrator.ts`, `mcp_server/lib/search/vector-index-schema.ts`, `shared/normalization.ts`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:48:- **Lines:** `memory-parser.ts:604-617`, `memory-save.ts:1055-1058, 1550-1553`, `chunking-orchestrator.ts:503-518`, `vector-index-schema.ts:1656-1659, 2226-2255`, `shared/normalization.ts:168-193`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:53:  - However, the database schema still allows `decision` and `discovery` in fresh installs, and low-level row serialization copies `memory.contextType` straight into `row.context_type` without normalization. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2226-2255`; `.opencode/skills/system-spec-kit/shared/normalization.ts:168-193`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:54:  - Upgraded databases are even looser: the migration adds `context_type` with no `CHECK` at all. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1656-1659`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:110:- fresh schema `CHECK(context_type IN (... 'planning', 'general', 'decision', 'discovery'))` still allows `decision`; [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2226-2255`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:111:- upgraded schemas may have **no** `CHECK` at all; [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:1656-1659`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:124:- `mcp_server/lib/search/vector-index-schema.ts` — schema still admits legacy values. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts:2226-2255`]
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/iterations/iteration-009.md:125:- `mcp_server/lib/search/vector-index-queries.ts` — search filters on raw `m.context_type = ?`. [SOURCE: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts:247-249`]
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:39:- `contentRouter_narrativeProgress_embeddingRescue_routesToWhatBuilt`: Given low-confidence rule output but strong similarity to progress prototypes, use Tier 2 and route to `what-built`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:56:- `contentRouter_narrativeDelivery_embeddingRescue_routesToHowDelivered`: Given low-confidence rules but high similarity to delivery prototypes, use Tier 2 and route to `how-delivered`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:74:- `contentRouter_decision_embeddingRescue_routesToDecision`: Given low-confidence rules but a strong decision-prototype match, use Tier 2 and route to a decision target.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:90:- `contentRouter_handoverState_embeddingRescue_routesToHandover`: Given low-confidence rules but strong similarity to handover prototypes, use Tier 2 and target `handover.md`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:107:- `contentRouter_researchFinding_embeddingRescue_routesToResearchDoc`: Given low-confidence rules but a strong prototype match for research text, use Tier 2 and route to research.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:124:- `contentRouter_taskUpdate_embeddingRescue_routesToTasks`: Given low-confidence rules but a strong match to task-update prototypes, use Tier 2 and route to tasks.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:143:- `contentRouter_metadataOnly_embeddingRescue_routesToContinuity`: Given low-confidence rules but a prototype match for metadata-only payloads, use Tier 2 and route to continuity.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:159:- `contentRouter_drop_embeddingSupportsDrop_keepsRefusal`: Given low-confidence rules but a prototype match for disposable chatter, use Tier 2 and keep the `drop` result.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:255:- `specDocStructure_dropClassification_returnsContam003`: Given a routed chunk that rule-based and embedding checks both resolve to `drop`, validate it and expect `SPECDOC_CONTAM_003`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:309:- `regression_embeddingSemanticSearch_paraphrasedQuery_returnsExpectedTopK`: Given a paraphrased semantic query, run vector retrieval and expect the intended canonical result in top-K.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/iterations/iteration-029.md:310:- `regression_fourStageSearchPipeline_allChannelsParticipateAndFuseCorrectly`: Given a fixture that activates trigger, BM25, FTS5, vector, and graph evidence, run the full pipeline and expect correct gather, fusion, rerank, and filter behavior.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/plan.md:36:- `getEmbeddingProfile()` (embeddings.js) - Returns provider's profile
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/plan.md:42:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/plan.md:51:    const embeddings = getEmbeddingsModule();
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/plan.md:52:    const profile = embeddings.getEmbeddingProfile();
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/plan.md:139:- **Add:** `test-embeddings-factory.js` entry
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:46:- **17 documentation fixes** applied (embedding-provider agnostic)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:95:| Deferred Indexing | Graceful degradation when embedding fails |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:114:- `VOYAGE_API_KEY` → "embedding API key"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:115:- `Voyage → Local → BM25` → `Primary API → Local → BM25-only`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:116:- Specific references to Voyage API → generic "embedding provider"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:147:- [x] Lazy model loading (T016-T019) - init_embeddings() deferred
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:150:- [x] BM25 hybrid search (T028-T031) - Pure JS implementation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:155:- [x] Cross-encoder reranking (T048-T051) - Voyage/Cohere/local providers
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:166:- [x] Fallback chain (T091-T095) - Primary API → Local → BM25-only
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:189:- `lib/search/vector-index.js` - Added schema v8 migration for causal_edges table
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:238:| `lib/search/bm25-index.js` | Pure JS BM25 implementation | ~380 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:239:| `lib/search/cross-encoder.js` | Voyage/Cohere/local reranking | ~490 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:243:| `lib/embeddings/provider-chain.js` | Embedding fallback chain | ~340 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/implementation-summary.md:290:| `mcp_server/lib/search/vector-index.js` | Schema v8 migration for causal_edges table |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-032.md:123:### T011 — getStartupEmbeddingDimension() fail-fast (vector-index-store.ts)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-032.md:127:`getStartupEmbeddingDimension` is imported at line 23 and used in `get_embedding_dim()` at lines 90-94. The pre-bootstrap dimension validation at lines 758-765 calls `validate_embedding_dimension_for_connection()`, and on mismatch throws `VectorIndexError` with `INTEGRITY_ERROR` code — correctly blocking DB bootstrap.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-032.md:129:**Minor concern:** `get_embedding_dim()` lines 90-95 contain a subtle logic inversion:
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-032.md:176:### T014 — executeMerge() upserts projection/lineage/BM25 (reconsolidation.ts)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-032.md:184:2. **BM25**: calls `bm25.removeDocument(String(existingMemory.id))` and `bm25.addDocument(String(newId), mergedBm25DocumentText)` at lines 338-339. A `repairBm25Document` fallback handles failure outside the transaction boundary at lines 364-374.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-032.md:209:2. A minor logic concern in `get_embedding_dim()` (lines 90-95) is flagged as P2 pending verification that `getStartupEmbeddingDimension()` itself reads `process.env.EMBEDDING_DIM`. If it does not, this becomes a P1 silent no-op for the env-var override path.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/research.md:39:1. **`contentRouter`** (`lib/routing/content-router.ts`) — classifies arbitrary session content into 8 categories using a 3-tier classifier (rule-based → embedding similarity → LLM escalation). Refuses to route at confidence <0.5.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/research.md:47:The `contentRouter` uses a 3-tier classifier (see iteration 2). Tier 1 rule-based handles ~80% of content. Tier 2 embedding similarity handles ~15%. Tier 3 LLM escalation handles ~5%. Low-confidence routes are refused and surfaced to the user. See `findings/routing-rules.md`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/003-continuity-refactor-gates/research/research.md:100:- **Gate A — Pre-work**: root packet backfill + embedding health check + backup
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:48:      "shared/embeddings.js",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:55:      "shared/embeddings/factory.js",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:57:      "shared/embeddings/providers/voyage.js",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:86:        "name": "embeddings.js",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:88:        "path": "shared/embeddings.js",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:130:        "path": "shared/embeddings/factory.js",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:142:        "path": "shared/embeddings/providers/voyage.js",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/graph-metadata.json:206:    "causal_summary": "SpecKit Reimagined synthesizes findings from 25 parallel agent analyses of 8 pre-analysis documents examining dotmd, seu-claude, drift, and system-speckit architectures. This specification defines 15 P0 blockers (10 original + 5 embedding resilience), 18 P1 requirements, and establishes a unified 6-7 week implementation roadmap to transform SpecKit into a best-in-class memory system with hybrid search, causal graphs, embedding resilience, and self-improvement capabilities.",
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/checklist.md:29:- [x] `vector-index.js` validation uses profile dimension instead of hardcoded 768
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/checklist.md:55:- [x] `memory_search()` returns relevant results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/checklist.md:56:- **Evidence:** Verified 2024-12-31: memory_index_scan completed (147 files). memory_search fix: context-server.js:676 changed `profile?.dimension` to `profile?.dim` (profile object uses `dim` property). Fix applied 2024-12-31 Attempt 2. MCP restart required to verify.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/checklist.md:115:- [x] `memory_search({ tier: 'constitutional' })` returns results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/checklist.md:130:- [x] `test-embeddings-factory.js` in SKILL.md inventory
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-022.md:8:**Issue** `hybridSearchEnhanced()` computes adaptive weights from a single aggregated `keywordResults` list, but then uses two different weighting schemes for the same lexical inputs. When only `vector`/`fts`/`bm25` are active, it returns `adaptiveResult.results` directly, so FTS and BM25 behave like one combined `keyword` channel with the full `keywordWeight`. As soon as an extra channel such as `graph` or `degree` is present, the code switches to `fuseResultsMulti(lists)` and evenly splits `keywordWeight` across FTS and BM25, regardless of how many results each channel actually returned. That makes the lexical share of RRF depend on whether an unrelated extra channel happened to be active, and it overweights sparse lexical channels when FTS/BM25 cardinalities differ.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-022.md:10:**Evidence** `hybrid-search.ts:998-1006` derives `keywordWeight` from `hybridAdaptiveFuse(semanticResults, keywordResults, intent)` and then blindly divides it by `lexicalChannelCount`; `hybrid-search.ts:1019-1023` bypasses those split weights entirely when the live channel set is only `vector`/`fts`/`bm25`, returning the aggregated adaptive results instead of the per-channel `lists`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-022.md:12:**Fix** Use one lexical weighting model everywhere. Either always fuse explicit per-channel lists with weights normalized from the actual active channels/result counts, or always collapse lexical channels into one list and remove the per-channel split path. Do not let the presence of `graph`/`degree` silently change how FTS and BM25 are weighted.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-022.md:23:### [P1] Confidence truncation drops candidates before later rerankers can promote them
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-022.md:43:The strongest issues here are all live-ranking consistency problems: lexical weighting changes depending on whether extra channels are present, Tier 2 fallback ignores explicit channel disables, confidence truncation runs before the later rerankers that can still improve recall, and token-budget enforcement is optimistic enough to exceed the budget it reports. I did not find a direct progressive-disclosure cursor-state corruption bug inside `hybrid-search.ts`; the continuation state itself lives in the handler/progressive-disclosure layer rather than this module.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-findings-registry.json:98:        "002-add-reranker-telemetry/decision-record.md:1-3",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-findings-registry.json:100:        "004-raise-rerank-minimum/decision-record.md:1-3",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-findings-registry.json:101:        "004-raise-rerank-minimum/implementation-summary.md:1-11"
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/deep-review-strategy.md:19:8. `mcp_server/lib/search/vector-index-schema.ts` — CHECK constraint includes "planning"
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-016.md:44:### [P2] Reconsolidation save path swallows BM25 indexing failure and commits a partially updated search state
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-016.md:49:The reconsolidation callback commits the memory row and metadata even when the BM25 lexical index update fails. Because the BM25 error is only logged and not propagated, recovery leaves the database and lexical search index out of sync.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-016.md:52:Inside the transaction in `reconsolidation-bridge.ts:216-261`, the handler indexes the vector row and metadata first, then attempts BM25 insertion at `248-255`. If `bm25.addDocument()` throws, the catch only logs `BM25 indexing failed (recon conflict store)` and continues to `recordHistory()` before returning the new `memoryId`. There is no rollback, no failed-state marker, and no immediate repair scheduling in that path, so the save can succeed while one retrieval channel is silently stale.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-016.md:55:Treat BM25 write failure as part of the atomic save contract and abort the transaction when it fails, or explicitly persist a degraded/index-pending state and trigger guaranteed follow-up repair. Logging alone is not sufficient recovery for a multi-index storage path.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-016.md:58:I found four meaningful issues in the error-handling and recovery surfaces. The highest-risk problems are incorrect error classification at the MCP boundary, direct leakage of internal exception text, and causal handlers returning unrelated canonical codes. I also found one state-recovery gap where reconsolidation can commit a memory while leaving BM25 indexing incomplete with only a warning log.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/tasks.md:34:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/tasks.md:39:- `getEmbeddingsModule()` (lines 42-47) provides lazy-loaded embeddings access
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/tasks.md:40:- `embeddings.getEmbeddingProfile()` exists and returns provider profile
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/tasks.md:53:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/tasks.md:67:- **File:** `.opencode/skills/system-spec-kit/mcp_server/lib/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/tasks.md:218:- [x] Constitutional files appear in `memory_search` results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/tasks.md:247:### T016: Document test-embeddings-factory.js
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:11:4. **RRF Search Fusion with BM25** (P1) - 40-50% relevance improvement
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:22:| **dotmd** | Triple-hybrid: Vector (LanceDB) + BM25 + Graph (LadybugDB) | Most comprehensive discovery |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:27:**Winner: dotmd** - Triple-engine approach with RRF fusion (k=60) and 1.5x graph weight discovers relationships pure vector+keyword misses.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:31:function rrfFusion(vectorResults, bm25Results, graphResults = [], k = 60, convergenceBonus = 0.10) {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:32:  const weights = { vector: 1.0, bm25: 1.0, graph: 1.5 };
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:46:  scoreSet(vectorResults, weights.vector, 'vector');
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:214:  search(embedding: number[], topK: number): Promise<SearchResult[]>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:215:  upsert(id: string, embedding: number[], metadata: object): Promise<void>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:237:| L1 | Orchestration | 2000-4000 | `memory_context` (new unified entry) |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:238:| L2 | Discovery | 200-500 | `memory_match_triggers`, `memory_stats` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:240:| L4 | Exploration | 500-1500 | `memory_search`, `memory_list` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:250:- Triple-hybrid search (vector + BM25 + graph) with RRF fusion
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:312:| Cross-encoder reranking | None | dotmd | **LOW** |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:339:| **BM25 Hybrid Search** | 7-10 days | Keyword retrieval | RRF |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:343:| **Query Expansion + Fuzzy Match** | 5-7 days | Typo tolerance | BM25 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:370:| 4-5 | Lazy Model Loading | 4-6h | Deferred embedding init |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:379:| 2-3 | BM25 Hybrid Search | 5d | FTS5 + vector combination |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:390:| 5-6 | Cross-Encoder Reranking | 5d | Top-20 reranking |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:408:├── RRF Search Fusion ───────┬──► BM25 Hybrid Search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:417:├── Cross-Encoder Reranking ◄──── RRF + BM25 (Phase 2)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:469:- Cross-encoder via `options.rerank`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:521:| Q3 | Cross-encoder selection: which provider? | Infra | Configurable; Voyage rerank-2 recommended for code/technical |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:573:      r.rerank_score *= penalty;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:591:  'memory_search': {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:592:    'E041': 'Run memory_index_scan to rebuild vector index',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:593:    'E001': 'Check embedding API key or set SPECKIT_LOCAL_EMBEDDINGS=true',
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:630:    memory_search: [
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:632:      { name: 'embedding_available', fn: checkEmbeddingProvider }
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:674:memory_search({ query: "session ${session.id}", anchors: ['state'] })
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:924:    rerank = false,
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:941:  // 3. Hybrid search (vector + BM25 + optional graph)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:942:  const [vectorResults, bm25Results, graphResults] = await Promise.all([
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:943:    vectorSearch(expandedQuery, limit * 3),
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:949:  let results = rrfFusion(vectorResults, bm25Results, graphResults, {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:951:    weights: { vector: 1.0, bm25: 1.0, graph: 1.5 },
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:969:  // 8. Cross-encoder reranking (optional)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:970:  if (rerank && results.length > 0) {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:971:    results = await rerankWithCrossEncoder(query, results.slice(0, 20));
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:991:      searchEngines: ['vector', 'bm25', options.includeGraph ? 'graph' : null].filter(Boolean),
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1076:    tools: ['memory_context'],
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1086:    tools: ['memory_match_triggers', 'memory_stats', 'memory_health'],
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1091:    tools: ['memory_search', 'memory_list', 'memory_browse'],
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1196:### 10.14 BM25-WASM Implementation Option
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1199:**Current in 082:** BM25 mentioned, WASM option missing
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1200:**Feature:** Use WebAssembly BM25 for performance
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1204:const BM25_WASM = require('bm25-wasm');
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1206:class BM25Index {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1208:    this.index = new BM25_WASM();
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1227:class BM25JS {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1240:function createBM25Index() {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1242:    return new BM25Index(); // WASM
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1244:    console.warn('BM25-WASM unavailable, using JS fallback');
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1245:    return new BM25JS();
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1250:**Impact:** 5-10x faster BM25 search with WASM
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1274:| BM25-WASM Implementation | 002-c | 4h | Faster BM25 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1293:function rrfFusion(vectorResults, bm25Results, graphResults = [], weights = {}, k = 60, convergenceBonus = 0.10) {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1294:  const { vector: wV = 1.0, bm25: wB = 1.0, graph: wG = 1.5 } = weights;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1308:  scoreSet(vectorResults, wV, 'vector');
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1379:_embedding_provider: EmbeddingProvider | None = None
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1381:def get_embedding_provider() -> EmbeddingProvider:
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1382:    global _embedding_provider
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1383:    if _embedding_provider is None:
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1384:        _embedding_provider = EmbeddingProvider(config)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1385:    return _embedding_provider
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1390:let embeddingProvider = null;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1393:  if (!embeddingProvider) {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1394:    embeddingProvider = await initializeEmbeddingProvider(config);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1396:  return embeddingProvider;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1412:  search(embedding: number[], topK: number): Promise<SearchResult[]>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1413:  upsert(id: string, embedding: number[], metadata: Record<string, unknown>): Promise<void>;
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1427:    private vectorStore: IVectorStore,
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1432:    const embedding = await this.embed(query);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/082-speckit-reimagined/consolidated-analysis.md:1433:    const vectorResults = await this.vectorStore.search(embedding, options.limit * 2);
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:47:The review ran in two passes. Iterations 001-020 covered the 20 primary dimensions from the spec: save pipeline, transaction safety, causal graph, hybrid search, embedding lifecycle, chunking, lineage, schema migrations, feature flags, memory parsing, checkpoints, shared memory, FSRS session learning, reconsolidation, query routing, error handling, index scan, graph signals, eval framework, and cross-cutting concurrency. Iterations 021-030 provided second-pass deep dives on the highest-density finding areas. The final synthesis in `review/review-report.md` classified all 121 findings: 5 P0 blockers, 75 P1 required fixes, 41 P2 deferred improvements.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:54:- **Embedding dimension guard** (`shared/embeddings/factory.js` + `lib/search/vector-index-store.ts`): `getStartupEmbeddingDimension()` in the shared factory resolves the canonical dimension at startup; `vector-index-store.ts` enforces a fail-fast guard on mismatch before DB bootstrap, rather than silently corrupting vectors.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:57:- **Reconsolidation merge reachability** (`lib/storage/reconsolidation.ts`): `executeMerge()` ensures the surviving memory is reachable: projection is upserted via `recordLineageTransition`, lineage is inserted via the same call, and BM25 is updated via remove/add with repair fallback. The bridge correctly returns `newMemoryId`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:61:Four parallel agents addressed the hybrid search pipeline and save pipeline. Key fixes: fallback threshold units kept as percentage-scale integers (30/17/10) with downstream conversion to fractional via `/ 100`; disabled channels no longer re-enter the fallback chain; `useGraph: false` correctly suppresses the degree channel; adaptive fusion lexical weight no longer inverts on high-lexical queries; confidence truncation deferred until after reranking; token-budget byte counter corrected. On the save side: PE filtering scoped to the caller's governance context; `atomicSaveMemory()` DB-first failure window closed; write lock scope extended across async reconsolidation; large-file chunking now passes through the quality gate. BM25 reconsolidation sync, archived-doc eviction, and live-update document shape all centralized via `buildBm25DocumentText()`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:73:The final sprint addressed the remaining 22 classified P1s plus two bonus defects discovered during integration. PE SUPERSEDE logic now chains only same-path supersedes; cross-path relationships become causal `supersedes` links. YAML body text no longer re-parses after frontmatter extraction. Anchor nesting validation enforces proper open/close pairing. Content normalization preserves checklist state markers. `memory_context` focused-mode applies intent-aware ranking. Resume mode detects intent from context rather than keyword matching. Handler errors return proper error responses instead of success-wrapping failures. Trigger matching adds a stopword filter and specificity check. Frontmatter extraction surfaces errors as structured failures. Chunked dedup hashes before the chunking decision. `task_postflight` scoped by `session_id`. Learning table allows multiple completed rows per `task_id`. `memory_match_triggers` scope fields are now wired to the matching logic. Graph degree self-loops counted once; degree-cache invalidation covers all mutation surfaces; degree cap enforced at 0.15 in RRF fusion. Incremental scan adds content-hash secondary detection. `SPECKIT_GRAPH_REFRESH_MODE=off` correctly disables graph enrichment. Eval dashboard per-channel breakdown preserved; ablation ground-truth alignment guard enforced. Bonus: stale projection eviction before replacement indexing (T088) and nested transaction failures converted to SAVEPOINTs (T088b).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:77:A 10-iteration meta-review (iterations 031-040) audited all prior work across correctness, security, traceability, and maintainability. It found 29 additional issues: 1 P0, 17 P1, 11 P2. Phase 12 fixed all 29 via 18 parallel GPT-5.4 Codex CLI agents. Key fixes: checkpoint restore now intersects spec_folder with tenant/user/agent/sharedSpace scope predicates (P0 F-001); token-budget truncation falls back to a summarized top result instead of returning empty; atomic save acquires the spec-folder mutex before promoting the pending file; PE filtering expands the vector search window until scoped matches are found; deferred chunk children receive their anchor identity; anchor extraction gates on validation before returning content; constitutional cache keys include the active DB path; schema DDL deduplicated through shared helpers; fallback policy consolidated into a single executor. Seven documentation drift P1s and five documentation P2s were fixed by updating spec.md, plan.md, checklist.md, implementation-summary.md, and tasks.md. Six code P2 advisories were fixed: embedding-cache dimension in PK, sessionId normalization, checkpoint tenantId trim guard, lineage row loader helper, structured rollback error metadata, and DB rebind error logging.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:83:**Concurrency (4 fixes):** Checkpoint restore maintenance barrier blocks mutations during restore lifecycle (T300). Shared-space upsert detects creation from INSERT result, not pre-read snapshot (T301). Reconsolidation validates predecessor unchanged after embedding await (T302). Scan cooldown converted from TOCTOU check to atomic lease with crash expiry (T303).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:85:**Search Performance (7 fixes):** Fallback pipeline split runs enrichment once on final tier (T310). Token estimation cached per-result in Map; JSON.stringify replaced with field estimator (T311). BM25 demoted to opt-in behind ENABLE_BM25; FTS5 is default lexical engine (T312). Degree scoring batched into single SQL (T313). Graph FTS rewritten as CTE + UNION ALL (T314). Adaptive fusion exposes getAdaptiveWeights() for single-pass fusionList (T315). MMR uses request-scoped embedding cache (T316).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:89:**Error Recovery (4 fixes):** Chunked PE supersede runs in single finalize transaction with compensating cleanup (T330). Safe-swap old-child deletion moved into finalization transaction (T331). Parent BM25 mutation delayed until chunk success (T332). bm25_repair_needed flag persisted for durable retry (T333).
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:100:| `lib/search/vector-index-store.ts` | Modified | P0+Sprint1: embedding dimension guard + concurrent DB switching fix |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:103:| `lib/storage/reconsolidation.ts` | Modified | P0: surviving memory upserts projection, lineage, BM25 on merge |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:107:| `lib/search/vector-index-mutations.ts` | Modified | Sprint1: active projection failures now fail-hard |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:111:| `lib/search/vector-index-schema.ts` | Modified | Sprint2: fail-hard DDL, compatibility check, v12/v23 migration repairs |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:112:| `lib/cache/embedding-cache.ts` | Modified | Sprint2: dimension-aware cache key |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/implementation-summary.md:113:| `shared/embeddings/` | Modified | Sprint2: structured provider cascade, effective provider tracking |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-strategy.md:45:- Re-reading `cross-encoder.ts`, `stage3-rerank.ts`, `content-router.ts`, and the regression suites prevented doc drift from being misreported as a shipped code defect (iterations 005, 006, 010).
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-strategy.md:56:- No P0-grade correctness or security defect was confirmed in `cross-encoder.ts`, `stage3-rerank.ts`, or `content-router.ts`; the material problems are packet closure and metadata integrity issues instead. Evidence: `.opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts:35-59,396-559`; `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:49-56,146-212`; `.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts:11-31`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/deep-review-strategy.md:91:| `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts` | correctness, security | 010 | 0 P0, 0 P1 | complete |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/review-report.md:63:- **Files**: `mcp_server/lib/search/vector-index-schema.ts`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/review/review-report.md:84:- **Files**: `mcp_server/lib/search/vector-index-schema.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-036.md:5:**Scope:** checkpoints.ts (handler), lineage-state.ts, access-tracker.ts, db-state.ts, reconsolidation.ts, vector-index-store.ts
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-036.md:18:A second vector is the checkpoint matching logic at lines 190–207 (handler): `checkpointMatchesScope` treats a scope field match as true when `actual === undefined`, meaning an unscoped checkpoint is accessible by any scoped caller. Combined with the storage-level folder-wide clear, a caller can present any tenant scope, pass scope validation against a scopeless checkpoint, and then trigger a folder-wide wipe.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-036.md:55:`executeMerge` wraps the main mutation (archive old, insert new, vec embed, causal edge, BM25, history) in a `db.transaction()` block at line 266. However, `recordLineageTransition(db, newId, {...})` is called at line 329 inside that transaction callback. The `recordLineageTransition` function itself calls `database.transaction(...)` internally (`lineage-state.ts:636`). In better-sqlite3, nested transactions are implemented as SAVEPOINTs. If the inner transaction (lineage) succeeds but the outer transaction subsequently rolls back (e.g., due to a BM25 failure at line 335 that throws), the inner SAVEPOINT is committed before the rollback occurs, leaving a lineage row referencing a `newId` that was never committed to `memory_index`. This produces an orphaned lineage entry pointing to a non-existent memory.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-036.md:60:- `reconsolidation.ts:335-345` — BM25 operations that can throw inside the same callback, after lineage is recorded
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-036.md:64:Either move `recordLineageTransition` to after the outer transaction commits (post-commit, similar to the BM25 repair path at lines 364-374), or ensure lineage-write exceptions cause the outer transaction to re-throw and roll back. A post-commit lineage write is simpler and removes the nested-savepoint concern entirely — if the memory insert commits, lineage is written; if the memory insert fails, no lineage is attempted.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-036.md:95:The vector-index database-connection-change listener at lines 140-149 calls `rebindDatabaseConsumers(database)` but discards the boolean return value. `rebindDatabaseConsumers` returns `false` when the session manager fails to initialize (lines 163-169). The listener path catches thrown errors but not a `false` return, so a failed rebind leaves some consumers on the new handle and others potentially stale, without any signal to the caller or calling handler.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-036.md:115:No new cross-tenant accumulator bleed was found in `access-tracker.ts` (the `init` guard at lines 63-67 correctly clears on DB swap). The `db-state.ts` constitutional-cache concern from previous iterations remains relevant in the `vector-index-store.ts` cache-key design but was not re-examined here as it was already classified.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:46:      "shared/embeddings/factory.js",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:47:      "lib/search/vector-index-store.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:56:      "lib/search/vector-index-mutations.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:60:      "lib/search/vector-index-schema.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:61:      "lib/cache/embedding-cache.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:81:        "path": "shared/embeddings/factory.js",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:85:        "name": "vector-index-store.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:87:        "path": "lib/search/vector-index-store.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:133:        "name": "vector-index-mutations.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:135:        "path": "lib/search/vector-index-mutations.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:157:        "name": "vector-index-schema.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:159:        "path": "lib/search/vector-index-schema.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:163:        "name": "embedding-cache.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/graph-metadata.json:165:        "path": "lib/cache/embedding-cache.ts",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/review-report.md:4:**Verdict: CONDITIONAL.** The 10-iteration review found **0 P0**, **7 P1**, and **0 P2** findings. The shipped code changes reviewed in `cross-encoder.ts`, `stage3-rerank.ts`, and `content-router.ts` did not surface a new runtime blocker, but the packet root is not a trustworthy closeout artifact yet because the root packet closure, root canonical docs, and migration-era metadata still drift.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/review-report.md:11:- key implementation files referenced by the packet: `cross-encoder.ts`, `stage3-rerank.ts`, `content-router.ts`, and the matching regression tests
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/review-report.md:35:| DRV-P1-004 | maintainability | Child decision records in phases `001-004` still say `status: planned` after packet completion. | `001-remove-length-penalty/decision-record.md:1-3`; `002-add-reranker-telemetry/decision-record.md:1-3`; `003-continuity-search-profile/decision-record.md:1-3`; `004-raise-rerank-minimum/decision-record.md:1-3` |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/004-search-fusion-tuning-review/review-report.md:54:No P0 finding was recorded. Candidate escalation paths were re-checked directly in `.opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts`, `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts`, and `.opencode/skills/system-spec-kit/mcp_server/lib/routing/content-router.ts`; none justified a blocker-grade security or correctness escalation.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/deep-research-dashboard.md:72:- CocoIndex semantic bootstrap timed out before producing usable hits, so iteration evidence came from direct reads and `rg`. (iteration 1)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:36:| `mcp_server/lib/vector-index.js` | Added `getEmbeddingDim()` function | 59-70 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:37:| `mcp_server/lib/vector-index.js` | Updated `indexMemory()` validation | 985 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:38:| `mcp_server/lib/vector-index.js` | Updated `updateMemory()` validation | 1102 |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:41:**Key Change:** Validation now uses dynamic dimension from embedding profile instead of hardcoded 768.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:58:| `SKILL.md` | Added test-embeddings-factory.js to scripts table |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:76:1. vector-index.js CRITICAL fix: PASS
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:84:9. SKILL.md test-embeddings: PASS
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:95:The CRITICAL dimension fix modifies `vector-index.js` which is loaded by the MCP server at startup. **The MCP server must be restarted** for the fix to take effect.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/implementation-summary.md:115:| `mcp_server/lib/vector-index.js` | Added dynamic dimension function |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/test-results-composite.md:104:| should combine vector and FTS results | FAIL | 0ms | Cannot read properties of undefined (reading 'fuse_results') |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/test-results-composite.md:106:| should mark results with in_vector and in_fts flags | FAIL | 0ms | Cannot read properties of undefined (reading 'fuse_results') |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/test-results-composite.md:110:| should include vector_rank and fts_rank | FAIL | 1ms | Cannot read properties of undefined (reading 'fuse_results') |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/test-results-composite.md:112:| should handle empty vector results | FAIL | 0ms | Cannot read properties of undefined (reading 'fuse_results') |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:7:`.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:13:`index_memory()` updates an existing row via `update_memory()` and then performs `upsert_active_projection()` outside that transaction, swallowing any error at lines 173-193. The insert path also catches and ignores projection failures inside the transaction at lines 217-221. `index_memory_deferred()` is not transactional at all and likewise ignores projection failures after both `UPDATE` and `INSERT` at lines 276-323. On the read side, the store’s prepared statements and counts all join `active_memory_projection` at `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts:395-438`, so a missing projection row makes the memory effectively vanish from normal list/count/search surfaces.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:20:`.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:26:The active connection is global at lines 308-321. `initialize_db()` immediately returns the global `db` when one is already active and no explicit `custom_path` is supplied at lines 598-610. The store instance only calls `initialize_db(this.dbPath)` once in `_ensureInitialized()` at lines 742-745, but later `upsert()` calls `index_memory()` at lines 800-844 and `delete()` calls `delete_memory()` at lines 856-859; those mutation helpers in `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts` reopen the database with plain `initialize_db()` at lines 131, 248, 340, 472, 542, and 584. That means whichever store most recently changed the global active connection wins.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:57:### [P2] Delete paths intentionally commit even when secondary vector cleanup fails
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:59:`.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:62:The delete flows treat failures in `vec_memories` cleanup as warnings, then continue deleting the primary `memory_index` row and return success. That creates an avoidable partial delete inside the same SQLite database: the metadata row is gone, but orphaned vector rows remain behind.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:65:`delete_memory_from_database()` catches `DELETE FROM vec_memories` failures and continues with the primary delete at lines 494-512. `delete_memories()` does the same thing inside the bulk transaction at lines 610-619, and only rolls back when the later `memory_index` delete fails. Since vector search joins `memory_index` to `vec_memories`, these orphan rows become integrity debris rather than a hard failure, which is why the bug can stay silent.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-002.md:68:Treat non-legacy vector deletion failures as fatal inside the transaction so the whole delete rolls back cleanly. If there is a strong reason to degrade gracefully, return an explicit partial-delete status and enqueue deterministic cleanup instead of returning an unqualified success.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-advisor-hook-brief-improvements/research/003-advisor-gap-investigation/iterations/iteration-02.md:9:- CocoIndex attempt:
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/findings-registry.json:210:      "id": "finding-3-5-public-code-graph-context-already-accepts-cocoindex-manual-graph-seeds-and-emits",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/findings-registry.json:211:      "text": "Public `code_graph_context` already accepts CocoIndex/manual/graph seeds and emits LLM-oriented neighborhoods, which is a good foundation for External Project-style richer context. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/context.ts:166]",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/findings-registry.json:607:      "id": "finding-9-6-defer-ladybugdb-storage-migration-embeddings-web-ui-parity-and-generated-ai-skil",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/findings-registry.json:608:      "text": "Defer: LadybugDB storage migration, embeddings, web UI parity, and generated AI skills until Public has measured bottlenecks or concrete UX need.",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/findings-registry.json:707:      "id": "ruled-out-1-1-cocoindex-semantic-bootstrap-timed-out-before-producing-usable-hits-so-iteration",
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-01/findings-registry.json:708:      "text": "CocoIndex semantic bootstrap timed out before producing usable hits, so iteration evidence came from direct reads and `rg`.",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/deep-research-strategy.md:13:- [ ] Q2: What performance bottlenecks exist in the hybrid search pipeline (token counting, fallback cascades, BM25 rebuild)?
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/deep-research-strategy.md:24:- Prior review dimensions: save pipeline, transactions, causal graph, hybrid search, embeddings, chunking, lineage, schema, feature flags, parsing, checkpoints, shared memory, FSRS, reconsolidation, query routing, errors, index scan, graph signals, eval, concurrency
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-advisor-hook-brief-improvements/research/003-advisor-gap-investigation/iterations/iteration-03.md:9:- CocoIndex attempt:
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/implementation-summary.md:67:7. **P1-8**: Removed legacy `decision`/`discovery` from CREATE TABLE CHECK constraints in both `vector-index-schema.ts` and `schema-downgrade.ts`.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/implementation-summary.md:83:| `mcp_server/lib/search/vector-index-schema.ts` | Modified | SCHEMA_VERSION 25, migration v25, strict CHECK constraint |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/implementation-summary.md:104:| Remove `!force` from `checkExistingRow` rather than adding UPSERT | Simplest fix that prevents duplicate accumulation. If content and metadata are identical, re-embedding produces the same result, so skipping is correct. |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/deep-research-strategy.md:14:- [x] Q3: Do the PARTIAL findings from the audit accurately identify all real discrepancies, or were some misclassified as MATCH? (false positives) -- **SUBSTANTIALLY ANSWERED**: PARTIAL findings identify real discrepancies, BUT ~50% of audit corrections contain errors (pointing to non-existent files/functions like fusion-lab.ts, title-builder.ts). Some MATCH classifications may also be overly generous (e.g., memory_search noted "15+ source files missing" yet classified MATCH).
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:35:| HIGH-004 | Sequential file reads | `mcp_server/lib/search/vector-index.js` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:183:**Location:** `mcp_server/lib/search/vector-index.js` lines 1529-1559
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:201:const result = vector_results.find(r => r.id === id) ||
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:207:**Resolution:** Added `vector_results_by_id` and `fts_results_by_id` Maps built upfront. Lookups are now O(1), reducing overall complexity from O(n*m) to O(n+m).
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:232:Constitutional memories are fetched inside `vectorSearch()` then fetched again in the handler.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:234:**Resolution:** Added check for existing constitutional memories before fetching. If already present in search results (via `vectorSearch`), the handler skips the redundant database query.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:240:**Location:** `mcp_server/lib/search/vector-index.js` lines 1193-1235
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:243:With 5 concepts (max), 10 embedding buffers totaling ~40KB per query.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:306:**Location:** `mcp_server/lib/search/reranker.js` lines 67-69
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:317:**Location:** `shared/embeddings.js` lines 158-168
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:368:**Location:** `mcp_server/lib/search/vector-index.js` lines 181-186
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/findings.md:487:**Location:** `mcp_server/lib/search/vector-index.js` lines 724-745
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-026.md:8:**Issue** `handleMemorySave()` runs preflight before the real save pipeline, but preflight's exact-duplicate check does not use the same-path exclusion, embedding-status filter, or governance-scope filter that the runtime dedup path uses. As a result, a legitimate same-path re-save can be rejected as an exact duplicate during preflight instead of reaching the runtime logic that would return `unchanged` or allow a metadata-only append-first update.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-026.md:10:**Evidence** `memory-save.ts:845-861` calls `runPreflight()` with only `content`, `spec_folder`, `database`, and `find_similar`, and `memory-save.ts:920-940` throws immediately when preflight fails. The exact-duplicate query in `preflight.ts:399-404` is only `WHERE content_hash = ? AND spec_folder = ? LIMIT 1`, so it has no same-path exclusion, no `parent_id IS NULL`, no `embedding_status` guard, and no tenant/user/agent/session/shared-space filtering. The runtime helpers do have those protections: `dedup.ts:93-148` handles same-path `unchanged`, while `dedup.ts:165-249` applies scope-aware cross-path dedup with healthy-status filtering and same-path exclusion. The current tests also reflect that split: `tests/content-hash-dedup.vitest.ts:323-544` exercises the runtime same-path and scope-aware cases, but `tests/preflight.vitest.ts:420-445` only verifies a generic hash match.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:84:- One script not documented: `test-embeddings-factory.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:132:- No content size limit before embedding generation
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:183:- `vector-index.js:53` hardcodes `EMBEDDING_DIM = 768`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:184:- Voyage provider returns 1024-dim embeddings
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:276:- `vector-index.js:53`: `const EMBEDDING_DIM = 768` (hardcoded, comment says "Legacy default")
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:277:- `vector-index.js:967`: Validation throws error if `embedding.length !== EMBEDDING_DIM`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:279:- Voyage embeddings rejected: "must be 768 dimensions, got 1024"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:349:2. `vector-index.js` has hardcoded `EMBEDDING_DIM = 768`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:350:3. Database schema created with 768-dim vectors
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/049-system-analysis-bugs/research/research.md:351:4. Voyage generates 1024-dim embeddings
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/graph-metadata.json:51:      "mcp_server/lib/search/vector-index-schema.ts",
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/graph-metadata.json:106:        "name": "vector-index-schema.ts",
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/009-reindex-validator-false-positives/graph-metadata.json:108:        "path": "mcp_server/lib/search/vector-index-schema.ts",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:14:I found 4 remaining recovery gaps. The strongest issue is in the chunked save + PE supersede path: the code can return an error after the new chunked memory tree is already committed, which makes retries likely to create duplicate or conflicting state. The other three gaps are recovery weaknesses around safe-swap cleanup and BM25 drift after partial failure.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:45:  - Only after that transaction commits does the code loop over `oldChildIds` and call `vectorIndex.deleteMemory(oldChildId)`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:56:### 3. Medium: all-chunks-failed rollback retains the old parent row but can leave BM25 indexed with the new parent summary
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:62:  - The parent BM25 document is updated before any chunk outcome is known.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:63:  - In the `successCount === 0` rollback branch, parent BM25 is removed only when `parentRolledBack === true`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:64:  - When re-chunking an existing parent (`parentRolledBack === false`), the code deletes staged child docs but does not restore the old parent BM25 document.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:66:  - The DB keeps the original parent row, but BM25 can now index the failed replacement summary.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:69:  - Delay parent BM25 mutation until at least one chunk succeeds and, for safe-swap, until finalization succeeds.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:70:  - Or capture the old parent BM25 payload and restore it explicitly in the `existing parent retained` rollback branch.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:72:### 4. Medium: reconsolidation merge commits DB changes even if BM25 remove/add fails twice
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:78:  - BM25 failures are caught and converted into `bm25RepairNeeded = true`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:82:  - The primary DB state is committed, but BM25 can be missing both the old and new document, or retain stale content depending on where the failure occurred.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:85:  - Keep BM25 mutation outside the DB transaction and make the repair path durable.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:86:  - At minimum, persist a repair-needed record or set a reconciliation flag on the merged row when BM25 repair fails.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-004.md:98:3. Add durable repair tracking for BM25 drift in chunking and reconsolidation paths.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-advisor-hook-brief-improvements/research/003-advisor-gap-investigation/iterations/iteration-01.md:9:- CocoIndex attempt:
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-010.md:61:  - stage2b-enrichment.ts, chunk-reassembly.ts, reranker.ts, fsrs.ts, search-utils.ts, deterministic-extractor.ts
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-010.md:68:- Scope: 2 PARTIAL findings. Verify memory_search "15+ source files" claim (questionable MATCH). Add handler-to-pipeline integration paths to audit scope.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:217:**File:** `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:223:  grep -n "safe_read_file_async\|fs.promises.readFile\|readFile.*async" ".opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.js"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:229:  grep -n "Promise.all" ".opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.js"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:235:  grep -B3 -A3 "readFileSync" ".opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.js" | grep -E "(for|while|forEach|map)"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:296:**Issue:** Constitutional memories fetched twice (in vectorSearch and handler)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:389:  node -e "require('./.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index'); console.log('vector-index: OK')"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:391:  **Expected:** "vector-index: OK"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:429:  test -f ".opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.js" && echo "EXISTS" || echo "MISSING"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/checklist.md:523:check "vector-index.js exists" 'test -f ".opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.js"'
./.opencode/changelog/agent-orchestration/v2.0.11.0.md:7:This part of the documentation needed to match the related files more closely. memory_search descriptions in the related file now consistently state the 3-channel hybrid pipeline (Vector, BM25, FTS5) with RRF fusion. This helps keep different copies of the same guidance from drifting apart.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-037.md:8:The seven targeted claims are all in-scope for this spec packet: lineage/versioning, embedding lifecycle, checkpoint lifecycle, shared memory/governance, reconsolidation, hybrid search, and causal graph correctness are explicitly listed in `spec.md:53-76`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-037.md:14:1. `implementation-summary.md:52` says fallback threshold units were "normalized from percentage to fractional", but the code still uses percentage units. `lib/search/hybrid-search.ts:234-239` defines fallback thresholds as `30`, `17`, and `10` with comments that explicitly say "percentage units", and `lib/search/vector-index-queries.ts:200` and `lib/search/vector-index-queries.ts:349` convert those values by dividing by `100` when building `max_distance`. This is a direct summary-to-code mismatch.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-037.md:19:2. `implementation-summary.md:45` over-attributes canonical embedding-dimension resolution to `lib/search/vector-index-store.ts`. That file does enforce the fail-fast bootstrap guard at `lib/search/vector-index-store.ts:207-235` and `lib/search/vector-index-store.ts:758-775`, but the imported `getStartupEmbeddingDimension()` resolves the canonical startup dimension in `shared/embeddings/factory.js:52-59` and `shared/embeddings/factory.js:198-199`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-037.md:21:4. `implementation-summary.md:48` is directionally right but imprecise. `executeMerge()` calls `recordLineageTransition()` and updates BM25 reachability, but the underlying operations are not all "upserts": active projection is upserted in `lib/storage/lineage-state.ts:357-377`, lineage is inserted in `lib/storage/lineage-state.ts:706-733`, and BM25 is handled as remove/add plus repair fallback in `lib/storage/reconsolidation.ts:335-373`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-037.md:28:| `getStartupEmbeddingDimension()` resolves canonical dimension | `implementation-summary.md:45` | `lib/search/vector-index-store.ts:90-109`, `lib/search/vector-index-store.ts:207-235`, `lib/search/vector-index-store.ts:758-775`, `shared/embeddings/factory.js:52-59`, `shared/embeddings/factory.js:198-199` | Partially verified | Canonical dimension resolution exists, and startup mismatch now fails before schema bootstrap. The resolution logic is in the imported shared factory, while `vector-index-store.ts` consumes it and enforces the fail-fast guard. |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-037.md:31:| `executeMerge()` upserts projection/lineage/BM25 | `implementation-summary.md:48` | `lib/storage/reconsolidation.ts:265-339`, `lib/storage/reconsolidation.ts:364-384`, `lib/storage/lineage-state.ts:357-377`, `lib/storage/lineage-state.ts:623-733` | Partially verified | `executeMerge()` creates the new memory row, calls `recordLineageTransition()` so projection is upserted and lineage is recorded, removes/adds BM25 documents, and returns `newMemoryId`. The word "upserts" is too broad for lineage and BM25. |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-037.md:32:| fallback threshold fractional not percentage | `implementation-summary.md:52` | `lib/search/hybrid-search.ts:234-239`, `lib/search/hybrid-search.ts:1565-1579`, `lib/search/hybrid-search.ts:1920-1947`, `lib/search/vector-index-queries.ts:200`, `lib/search/vector-index-queries.ts:349` | Not verified | Current code still expresses fallback thresholds as percentages and converts them downstream via `/ 100`. |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/checklist.md:67:- [x] CHK-008 [P0] Highest-risk recent surfaces are re-tested first before downstream standards docs are touched [EVIDENCE: Phase 4/5 — memory-save, memory-index, shared-memory, vector-index-store, session-manager, generate-context, workflow all retested and passing]
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-005.md:15:  - `.opencode/skills/system-spec-kit/shared/embeddings.ts:307-313` documents `SPECKIT_EAGER_WARMUP` / `SPECKIT_LAZY_LOADING` as inert and hard-returns `false` from `shouldEagerWarmup()`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-advisor-hook-brief-improvements/research/003-advisor-gap-investigation/research.md:40:- CocoIndex was attempted with repo-local root overrides, but the CLI daemon could not start cleanly inside this sandbox. I still recorded the exact attempted queries in the iteration logs and completed the evidence pass with exact grep plus local code-graph SQLite.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-004.md:78:Similarly, `lib/search/vector-index` (21 importers, 5 catalog mentions) and `lib/providers/embeddings` (11 importers, 23 catalog mentions) are heavily cross-cutting but were audited per-consumer, not as independent units.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-004.md:87:- `memory_search` classified MATCH in 001-retrieval, but it imports `tier-classifier.ts` (0 catalog mentions) and `attention-decay.ts` (0 catalog mentions)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-004.md:89:- `memory_context` classified MATCH in 001-retrieval, but it imports `pressure-monitor.ts` (0 catalog mentions)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-004.md:101:| 15-25 imports | 4 | envelope (19), vector-index (21), hooks (17), memory-parser (14) | Cataloged but per-consumer only |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-004.md:102:| 7-12 imports | 5 | cognitive (12), embeddings (11), search-flags (10), history (10), trigger-matcher (7), causal-edges (7) | Mixed: some cataloged, 3 cognitive modules uncataloged |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/002-content-routing-accuracy-research/iterations/iteration-004.md:4:- Focus: adversarially re-check the live Stage 3 rerank path
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/002-content-routing-accuracy-research/iterations/iteration-004.md:5:- Files reviewed: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/002-content-routing-accuracy-research/iterations/iteration-004.md:11:- The live rerank path still reads `config.adaptiveFusionIntent ?? config.detectedIntent ?? ''`, which confirms the old 001 verdict is stale evidence rather than a current defect. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209]
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-001.md:67:`reconsolidate()` chooses `topMatch` from a similarity search, and `executeMerge()` then reads the predecessor row plus vector row before awaiting embedding generation. After that await, it archives `existingMemory.id` and inserts the merged successor using the stale pre-await row contents. If another writer updates, supersedes, or deletes that same memory during the embedding gap, the merge path can overwrite fresher metadata, archive an already-changed predecessor, or fork from a stale content snapshot without noticing.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-001.md:76:Earlier reconsolidation findings in this packet focused on wrong IDs, orphaned lineage, and BM25/projection correctness. I did not find one covering this stale-snapshot race in the merge path itself.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-001.md:111:- P1: reconsolidation merge acts on a stale predecessor snapshot after an async embedding gap
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:20:const vector_results_by_id = new Map();
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:21:vector_results.forEach(r => vector_results_by_id.set(r.id, r));
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:30:const result = vector_results_by_id.get(id) || fts_results_by_id.get(id);
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:34:- [x] `vector_results_by_id` Map exists (line 34)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:118:  // memories from its vectorSearch call.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:126:    const constitutional_results = vectorIndex.vectorSearch(query_embedding, {
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:156:**File:** `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.js`
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-5-8.md:178:- No embedding-based query analysis
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/review-011-pass-b.md:19:| Jargon explained | Fail | Some terms are still too insider-facing or unexplained on first use, especially `CocoIndex Code`, `Code Graph`, `MCP`, and `FTS5`. BM25 and RRF are explained well, but the same standard is not applied consistently. |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/review-011-pass-b.md:26:- Some first-use jargon is still unexplained. Replace or define terms like `CocoIndex Code`, `Code Graph`, `MCP`, and `FTS5` for a smart non-developer reader.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:1:# Iteration 027: BM25 index rebuild and consistency
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:5:### [P1] Reconsolidation merge mutates `memory_index` without syncing the in-memory BM25 singleton
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:8:**Issue** The merge path archives the old row and inserts a replacement row directly in `memory_index`, but it never removes the archived document from the in-memory BM25 index or adds the merged replacement. The bridge then returns early, so the normal save path that would at least call `bm25.addDocument(...)` never runs. That leaves the process-local BM25 index out of sync with the database until a restart or a full rebuild happens.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:10:**Evidence** `reconsolidation.ts:223-262` sets `is_archived = 1` on the old row and inserts a new merged row into `memory_index`, but there is no BM25 mutation in that transaction. `reconsolidation-bridge.ts:271-313` treats `merge` as fully handled and exits before the normal create-record path executes. By contrast, the canonical rebuild path in `bm25-index.ts:289-313` only indexes rows where `COALESCE(is_archived, 0) = 0`, so the live singleton can keep returning an archived document that the rebuilt index would exclude while also omitting the new merged row entirely.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:12:**Fix** Add an explicit BM25 sync step for reconsolidation merges after the DB transaction commits: remove `existingMemory.id`, add `newMemoryId` using the same text composition as `rebuildFromDatabase()`, or call a scoped rebuild helper for the affected IDs. Do not rely on restart-time rebuilds for this path.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:14:### [P1] Live BM25 updates do not index the same document shape that rebuilds and FTS scoring use
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:17:**Issue** The rebuild path indexes `title + normalized content_text + trigger_phrases + file_path`, but most live mutation paths feed the singleton only raw content or summary text. That means the in-memory BM25 index has different tokens, different normalization, and effectively different field weighting than the DB-backed rebuild/FTS paths. Queries that depend on title, trigger phrases, file-path terms, or normalized markdown content can therefore behave differently before and after a rebuild.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:19:**Evidence** `bm25-index.ts:41-55` defines field weights with title as the strongest signal, and `bm25-index.ts:289-313` rebuilds documents from `title`, `normalizeContentForBM25(content_text)`, `trigger_phrases`, and `file_path`. The steady-state mutation paths do not mirror that shape: `create-record.ts:201-205` indexes only `parsed.content`, `lineage-state.ts:385-388` indexes only `parsed.content`, `chunking-orchestrator.ts:244-248,341-345` indexes only `parentSummary` or `chunk.content`, `memory-crud-update.ts:155-169` reindexes only on title/trigger edits and still skips `normalizeContentForBM25`, and `archival-manager.ts:424-448` re-adds unarchived rows without normalization. Because `BM25_FTS5_WEIGHTS` are explicitly "not the in-memory BM25 engine" (`bm25-index.ts:41-42`), the runtime BM25 channel never actually matches the weighted field model that rebuilds and FTS search assume.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:21:**Fix** Centralize BM25 document construction behind one helper, for example `buildBm25DocumentText(row)` inside `bm25-index.ts`, and use it everywhere: rebuilds, saves, updates, chunking, lineage writes, and unarchive. That helper should include the same fields and `normalizeContentForBM25()` call every time. If field weighting is intended for the in-memory engine too, encode fields separately or simulate the weights during token construction instead of silently dropping them in live updates.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:23:### [P1] Assistive auto-merge archives rows in SQL but never evicts them from BM25, so the singleton can grow with stale archived documents
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:26:**Issue** Assistive auto-merge marks the older memory as archived with a direct `UPDATE`, but it does not call the BM25 archive sync used elsewhere. The save then continues normally and indexes the new memory, so the singleton keeps the archived old document and adds the replacement. Over repeated near-duplicate saves this causes stale archived entries to accumulate in memory even though the authoritative rebuild path would exclude them.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-027.md:34:The highest-risk consistency problems are in reconsolidation and assistive archive flows, which mutate `memory_index` without applying the BM25 sync rules that startup and checkpoint restore already use. I also found a broader parity issue: live BM25 updates are indexing a different document shape from the canonical rebuild path, so title/trigger/file-path relevance and normalized content behavior can change depending on whether the process has rebuilt recently.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:4:Q2: Performance bottlenecks in the hybrid search pipeline, with emphasis on token counting efficiency, fallback cascade overhead, BM25 rebuild cost, vector-search-adjacent latency, graph/degree overhead, and fusion computation.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:21:  - `hybridSearchEnhanced()` does much more than candidate collection: degree scoring, channel enforcement, reranking, co-activation, folder scoring, confidence truncation, context-header injection, and token-budget truncation: [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1046), [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1246), [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1458), [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1482)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:24:  - Queries that degrade from tier 1 to tier 2 or from primary to retry pay for vector retrieval, lexical retrieval, degree computation, MMR embedding fetches, co-activation, folder scoring, trace enrichment, and token-budget accounting multiple times before a final result is even chosen.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:28:  - For fallback stages, use `stopAfterFusion: true` or a dedicated pre-ranking path, evaluate degradation on fused candidates, then run reranking/enrichment/token truncation only once on the final merged candidate set.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:44:### 3. The in-memory BM25 engine is still a full-corpus scan, and rebuilds are synchronous full reindexes
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:47:  - Each `BM25Index.search()` iterates every indexed document and computes score document-by-document: [bm25-index.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts#L312)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:55:  - Treat FTS5 BM25 as the default lexical engine and demote the in-memory BM25 path to a narrow fallback or experimental channel.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:99:### 7. Vector-search-adjacent latency is amplified by re-fetching embeddings for MMR after retrieval
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:102:  - The vector channel already runs before fusion: [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L981)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:103:  - Later, MMR issues a second database read to fetch embeddings from `vec_memories` for the reranked IDs, then rebuilds `Float32Array` views and does per-candidate lookups: [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1260), [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1272), [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1305)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:104:  - The `diversified.map(... reranked.find ...)` merge is also an avoidable O(n^2) pass, even if `n` is usually small: [hybrid-search.ts](/Users/michelkerkmeester/MEGA/Development/Opencode Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/hybrid-search.ts#L1305)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:106:  - Fallback queries can execute vector retrieval multiple times, then still pay an extra embedding fetch for MMR.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:109:  - Let the vector channel optionally return embedding buffers for the top-K hits, or maintain a request-scoped embedding cache keyed by memory ID.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:110:  - Replace `reranked.find(...)` with a `Map` built once from reranked IDs.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:114:- The best near-term win is to make fallback operate on pre-enrichment candidates and defer reranking, trace/header injection, and token-budget truncation until the final tier is chosen.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-002.md:115:- The next highest-value change is to shrink lexical and graph-side synchronous DB work: reduce dependence on the in-memory BM25 full scan, batch degree computation, and rewrite the graph FTS join to avoid OR-based duplication.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-1-4.md:186:**vector-index.js (Lines 139-155) - Async function:**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-1-4.md:207:**vector-index.js (Lines 1545-1549) - Promise.all in query search:**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-1-4.md:216:**vector-index.js (Lines 1621-1624) - Promise.all in concept search:**
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-1-4.md:224:**vector-index.js (Lines 1693-1696) - Promise.all in trigger match:**
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/002-content-routing-accuracy-research/iterations/iteration-014.md:4:- Focus: re-check the live Stage 3 rerank implementation against the promoted 001 review claim
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/002-content-routing-accuracy-research/iterations/iteration-014.md:5:- Files reviewed: `.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts`, `001-search-fusion-tuning/review/review-report.md`
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/002-content-routing-accuracy-research/iterations/iteration-014.md:6:- Tool log (8 calls): read config, read state, read strategy, read live rerank implementation, read promoted 001 review report, grep intent lambda map, reread exact intent selection line, update correctness notes
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/review/002-content-routing-accuracy-research/iterations/iteration-014.md:11:- The rerank implementation still derives the effective intent from `adaptiveFusionIntent` before `detectedIntent`, which confirms the promoted 001 report is historical carry-over rather than a live bug report. [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage3-rerank.ts:209]
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/005-speckit-consolidation/scratch/legacy-memory-quarantine/17-12-25_00-00__speckit-consolidation-complete.md:391:| Memory Not Found | Search returns no results | Check `memory_search({ specFolder: "** `specs/004-speckit/003-speckit-consolidation/`" })` |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/005-speckit-consolidation/scratch/legacy-memory-quarantine/17-12-25_00-00__speckit-consolidation-complete.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/005-speckit-consolidation/scratch/legacy-memory-quarantine/17-12-25_00-00__speckit-consolidation-complete.md:514:embedding_model: "nomic-ai/nomic-embed-text-v1.5"
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/005-speckit-consolidation/scratch/legacy-memory-quarantine/17-12-25_00-00__speckit-consolidation-complete.md:515:embedding_version: "1.0"
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/review-008-pass-b.md:19:| Jargon explained | Fail | Some terms are not explained on first use, including `agent dispatches`, `orphaned vectors` in the summary, `trigger_phrases`, `JSON arrays`, and `runtime`. |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/review-008-pass-b.md:24:- The summary uses unexplained technical phrasing, especially `8 GPT-5.4 Copilot agent dispatches`, `orphaned vectors`, and `175/175 in-scope folders`.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-advisor-hook-brief-improvements/research/003-advisor-gap-investigation/deep-research-state.jsonl:2:{"type":"iteration","iteration":1,"status":"completed","focus":"advisor_recommend downstream docs/tests around new workspaceRoot + effectiveThresholds contract","newInfoRatio":0.75,"timestamp":"2026-04-24T09:53:42Z","findingsNew":["F-003","F-004","F-007"],"graphEvents":["CocoIndex CLI attempted with repo-local root override but daemon startup was blocked in sandbox; continued with exact grep + local code-graph SQLite"],"notes":["Feature catalog and manual playbook still describe the older recommend output shape","Recommend handler test does not assert the new public fields"]} 
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-001.md:10:- L1 (memory_context) -> Catalog 01-retrieval
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-001.md:11:- L2 (memory_search, memory_quick_search, memory_match_triggers, memory_save) -> Catalog 01-retrieval + 02-mutation
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:14:- [`vector-index-schema.ts:935`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L935) enforces `UNIQUE(logical_key, version_number)` in `memory_lineage`, and [`vector-index-schema.ts:999`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L999) makes `logical_key` the primary key of `active_memory_projection`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:25:- [`pe-gating.ts:63`](../../../../../../skill/system-spec-kit/mcp_server/handlers/pe-gating.ts#L63) finds similar memories by semantic search within scope, not by same-path identity.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:33:**File**: `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:40:- [`vector-index-schema.ts:1063`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L1063) stores and indexes `retention_policy` / `delete_after`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:41:- [`vector-index-mutations.ts:43`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts#L43) deletes `memory_lineage` rows outright and [`vector-index-mutations.ts:66`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-mutations.ts#L66) deletes the matching `active_memory_projection`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:42:- [`vector-index-queries.ts:84`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts#L84) and [`vector-index-store.ts:492`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L492) show that folder reads, counts, and constitutional injection all rely on `JOIN active_memory_projection`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:55:- [`vector-index-schema.ts:948`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L948) and [`vector-index-schema.ts:1000`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L1000) make that ambiguous string a uniqueness/primary-key boundary.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-007.md:67:- [`vector-index-schema.ts:948`](../../../../../../skill/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L948) enforces uniqueness on `(logical_key, version_number)`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:7:- `.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:24:  - `checkContentHashDedup()` repeats the same nullable-scope pattern on top of `spec_folder`, `content_hash`, `parent_id IS NULL`, and `embedding_status IN (?, ?)`, again with `ORDER BY id DESC LIMIT 1`: [dedup.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/save/dedup.ts#L188), [dedup.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/save/dedup.ts#L216)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:26:  - The schema only provides separate indexes for `spec_folder`, `content_hash`, `canonical_file_path`, and a broad governance scope tuple; it does not provide a composite index aligned to these dedup predicates: [vector-index-schema.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L2261), [vector-index-schema.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L2271), [vector-index-schema.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L2277)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:29:  - This sits on the hottest write path in the server and is paid before the save even reaches embedding, PE gating, or insert/update work.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:33:  - Add a composite partial index for the content-hash path, for example `(spec_folder, content_hash, embedding_status, tenant_id, user_id, agent_id, session_id, shared_space_id, id DESC) WHERE parent_id IS NULL`, and consider a sister index for exact-path dedup keyed by `(spec_folder, canonical_file_path, id DESC)` plus a file-path fallback.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:39:  - On the next cache miss, `trigger-matcher` loads every row whose `trigger_phrases` is non-empty and `embedding_status = 'success'`: [trigger-matcher.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/parsing/trigger-matcher.ts#L339)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:40:  - The schema has `idx_embedding_status`, but there is no partial index tuned to the actual trigger-cache source predicate (`trigger_phrases IS NOT NULL`, not `'[]'`, not `''`, and `embedding_status = 'success'`): [vector-index-schema.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L2264)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:45:  - Add a partial index aligned to the source query, for example `CREATE INDEX IF NOT EXISTS idx_trigger_cache_source ON memory_index(embedding_status, id) WHERE embedding_status = 'success' AND trigger_phrases IS NOT NULL AND trigger_phrases != '[]' AND trigger_phrases != ''`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:69:  - `buildTimeline(specFolder)` filters by `spec_folder` and sorts by `created_at DESC`, but the schema only has separate indexes on `spec_folder` and `created_at`, not a composite `(spec_folder, created_at DESC)`: [temporal-contiguity.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/temporal-contiguity.ts#L163), [vector-index-schema.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L2261), [vector-index-schema.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L2262)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/iterations/iteration-003.md:83:  - The schema has `idx_file_path`, but a leading-wildcard `LIKE` cannot use it effectively: [vector-index-schema.ts](/Users/michelkerkmeester/MEGA/Development/Opencode%20Env/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts#L2277)
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/verification/high-fixes-9-12.md:61:"_NOTE_1_DATABASE": "Stores vectors in: .opencode/skills/system-spec-kit/database/context-index.sqlite",
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:11:- `mcp_server/lib/search/vector-index-schema.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:12:- `mcp_server/lib/cache/embedding-cache.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:25:`PRIMARY_FALLBACK_MIN_SIMILARITY = 30` and `SECONDARY_FALLBACK_MIN_SIMILARITY = 17` at lines 235-239 are intentionally in percentage units (0-100 scale). This is consistent with the vector-index-queries layer, which converts at line 200: `const max_distance = 2 * (1 - minSimilarity / 100)`. The constants are passed directly as `minSimilarity` to `vectorSearchFn`, which internally divides by 100 before converting to cosine distance. The pe-gating layer also passes `minSimilarity: 50` (line 83 in pe-gating.ts) using the same 0-100 scale. No unit mismatch exists.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:33:**Residual concern (P2):** `forceAllChannels` in `hybridSearchEnhanced()` at line 849-850 replaces `activeChannels` with the full `allPossibleChannels` set (`['vector', 'fts', 'bm25', 'graph', 'degree']`) before the `allowedChannels` cap is applied at lines 854-857. Removing from `activeChannels` happens after the set is fully populated. The gate is present and correct, but the logic reads confusingly — `forceAllChannels` populates the full set first and then the mask removes from it, rather than starting from `allowedChannels` directly. No functional bug but the ordering creates maintenance risk.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:52:`hybridAdaptiveFuse()` is called at line 1033 with `semanticResults` and `keywordResults` as positional arguments. The resulting `adaptiveResult.weights` at line 1034 extracts `semanticWeight`, `keywordWeight`, and `adaptiveGraphWeight`. These are then applied at lines 1042-1048: the vector list gets `semanticWeight`, the graph list gets `adaptiveGraphWeight`, and a synthesized keyword list gets `keywordWeight`. The fusion list explicitly excludes `fts` and `bm25` sources (line 1040) before injecting the merged keyword bucket. No weight-argument transposition is present.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:54:#### Fix 5: Confidence truncation after rerankers
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:59:1. Cross-encoder / local reranker (lines 1170-1175)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:60:2. MMR reranking (lines 1177-1243)
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:66:Confidence truncation correctly runs after all reranking and score-boosting steps. The `evaluationMode` bypass at line 1305 prevents truncation in eval scenarios. The implementation matches the intended sequencing.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:86:`BM25Index.rebuildFromDatabase()` at lines 354-383 uses:
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:94:**Gap (P2):** The online path (`addDocument` / `removeDocument`) does not check `is_archived` — individual saves or ingest calls can add archived documents to the in-memory index. Only a full `rebuildFromDatabase()` guarantees exclusion. This is a known limitation noted in the comment block but creates a window where BM25 returns archived hits between restarts.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:100:`buildBm25DocumentText()` is defined at lines 205-226 and exported at line 518. `rebuildFromDatabase()` at line 371 calls it directly. The chunking-orchestrator at lines 248-253 and 355-360 also imports and calls `bm25Index.buildBm25DocumentText(...)`. The normalization of `trigger_phrases` (JSON array or raw string) is handled by `normalizeTriggerPhrasesForBM25()` at lines 175-203, centralized within the same module. Duplication is eliminated.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:132:`withSpecFolderLock()` at line 463 is called with `prepared.parsed.specFolder` as the key. The entire indexing pipeline — embedding, PE gating, DB write — executes within this lock. The `refreshFromDiskAfterLock` path at line 465-466 re-parses the file after acquiring the lock to eliminate TOCTOU between the pre-lock parse and the locked write. The lock scope is appropriate.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:138:`isSaveQualityGateEnabled()` and `isQualityGateEnabled()` at line 514 gate the quality check. The quality gate at lines 516-571 runs after embedding generation and before PE gating — the ordering is correct. The `qualityGateMode === 'warn-only'` path at line 540 passes spec documents through with a warning rather than hard-rejecting them, which is the intended behavior for live spec documents. Errors inside the quality gate at lines 566-570 are caught and logged without blocking the save.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:170:### vector-index-schema.ts — Fail-hard DDL and v12/v23 migration repairs
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:208:### embedding-cache.ts — Dimension-aware cache key
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:216:SELECT embedding FROM embedding_cache WHERE content_hash = ? AND model_id = ? AND dimensions = ?
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:220:**P1 finding:** The primary key does not include `dimensions`. `storeEmbedding()` at line 128-133 uses `INSERT OR REPLACE`, keyed on `(content_hash, model_id)`. If the same content is re-embedded with a different model that produces a different dimension count (e.g., model upgrade from 1536-dim to 3072-dim embeddings), `INSERT OR REPLACE` will overwrite the old entry. The `lookupEmbedding` call with the new `dimensions` value will then find the new entry correctly. However, if the model produces the same `model_id` string with a different `dimensions` value (dimension mismatch bug in the provider), `INSERT OR REPLACE` will silently replace the correctly-dimensioned embedding with the wrong one. The `lookupEmbedding` dimension filter prevents returning wrong-dimension embeddings on read, but the store step can silently corrupt a valid cache entry with an identically-named model that returns different dimensions. This is an edge case but represents a correctness risk for deployments that modify embedding models without changing the model ID string.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:230:`chunkLargeFile()` is imported from `'../lib/chunking/anchor-chunker'` (line 18). The `indexChunkedMemoryFile()` function passes `chunk.label` as `anchorId` at line 306 to `vectorIndex.indexMemory()`. Each chunk carries its label through `applyMetadata` at line 334 (`chunk_label: chunk.label`). The parent is created with `embedding_status: 'partial'` at line 230 and the summary text as `contentText` at line 213. The anchor-mode semantics are implemented end-to-end.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:236:Each child insert is wrapped in `insertChunkTx = database.transaction()` at lines 301-345. The transaction covers both `vectorIndex.indexMemory()` (or `indexMemoryDeferred()`) and `applyMetadata()`. If `applyMetadata` throws, the insert rolls back.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:257:| 5 | hybrid-search.ts | Confidence truncation after rerankers | VERIFIED | — |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:267:| 15 | vector-index-schema.ts | Fail-hard DDL | VERIFIED | — |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:268:| 16 | vector-index-schema.ts | v12 migration repair | VERIFIED | — |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:269:| 17 | vector-index-schema.ts | v23 migration repair | VERIFIED | P2 residual |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:270:| 18 | embedding-cache.ts | Dimension-aware cache key | VERIFIED | P1 new finding |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:281:**File:** `.opencode/skills/system-spec-kit/mcp_server/lib/cache/embedding-cache.ts:38-48`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:283:The `embedding_cache` table defines `PRIMARY KEY (content_hash, model_id)`. The `storeEmbedding()` function uses `INSERT OR REPLACE` (line 128), which replaces an existing `(content_hash, model_id)` entry regardless of the `dimensions` value. If a model ID is reused with a different dimension count (e.g., A/B model testing, silent provider config change), a store call with the new dimension will silently overwrite the correctly-dimensioned cached embedding. The `lookupEmbedding()` dimension filter protects reads, but the corrupt entry remains in the cache and blocks future correct-dimension lookups until eviction.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:321:When `useSafeSwap` is true during re-chunking, child records are inserted with `parent_id = NULL`. If the process crashes before the parent-swap finalization step, these NULL-parent children become permanent orphans in `memory_index`. They consume storage, are included in BM25 index results (since BM25 rebuild reads all non-archived rows without filtering by `parent_id IS NOT NULL`), and cannot be garbage-collected by parent-cascade DELETE.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:323:**Fix:** Add a startup or maintenance-mode query to detect and clean up NULL-parent chunk rows: identify rows where `chunk_index IS NOT NULL AND parent_id IS NULL AND embedding_status IN ('success', 'pending')` and either assign them to their parent (if recoverable by `file_path` match) or delete them.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:325:### P2-033-E — BM25 in-memory index can contain archived documents between restarts
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-033.md:330:`rebuildFromDatabase()` correctly filters `WHERE COALESCE(is_archived, 0) = 0`. However, `addDocument()` has no archive check. When `memory-save.ts` or the ingest path calls `bm25.addDocument()` for a record that is simultaneously being archived, the in-memory index is updated with the archived content and will continue returning it until the next server restart (which triggers a fresh rebuild). Queries against the BM25 index can therefore surface archived content within the same server session.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:36:| C-3 | P1 | Reconsolidation merge uses a stale predecessor snapshot after an async embedding gap — no compare-and-swap guard | reconsolidation.ts |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:45:| S-3 | High | In-memory BM25 is a full-corpus scan; rebuilds are synchronous full reindexes blocking startup | bm25-index.ts |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:49:| S-7 | Medium | MMR re-fetches embeddings from DB after vector channel already retrieved them | hybrid-search.ts |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:68:| E-3 | Medium | All-chunks-failed rollback can leave BM25 indexed with the new parent summary when existing parent is retained | chunking-orchestrator.ts |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:69:| E-4 | Medium | Reconsolidation merge commits DB changes even if BM25 remove/add fails; no durable repair queue | reconsolidation.ts |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:75:| D-1 | Low | Dead eager-warmup branch still shipped; flag hook is inert | context-server.ts, embeddings.ts |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:91:6. **S-3**: Demote in-memory BM25 to fallback; use FTS5 as default lexical engine
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/research/research.md:100:13. **E-4**: Persist BM25 repair-needed flag when repair fails
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-02/iterations/iteration-001.md:30:- External Project `query` is positioned as process-grouped graph intelligence using hybrid BM25 plus semantic vector search, with Reciprocal Rank Fusion, optional task/goal ranking context, group mode, and service scoping [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/src/mcp/tools.ts:49] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/src/mcp/tools.ts:61] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/src/mcp/tools.ts:63].
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/002-memory-quality-remediation/research/deep-research-strategy.md:74:- Does NOT validate or improve embedding model selection (Voyage-4 is fine)
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/review-006-pass-a.md:8:| Replace residual `__dirname` usage in `map-ground-truth-ids.ts` and `reindex-embeddings.ts` | Yes | Covered under `Runtime Correctness` -> `Wrapper scripts still depended on CommonJS path behavior`. |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/review-006-pass-a.md:11:| Fix `shared/package.json` root export and add `./embeddings` subpath | Yes | Covered under `Runtime Correctness` -> `The shared package root export pointed at the wrong output`. |
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/review-006-pass-a.md:19:| Add a cached lazy loader for vector-index imports in `vector-index-store.ts` | Yes | Covered under `Performance` -> `Hot-path vector index imports were being reloaded too often`. |
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:5:### [P1] `memory_match_triggers` cannot accept the scope fields its handler depends on
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:10:**Evidence** `tool-schemas.ts:209-213` defines the public `memory_match_triggers` input schema without any scope fields. `tools/types.ts:96-103` mirrors that narrow shape. But `handlers/memory-triggers.ts:104-115` declares those scope fields as supported inputs, and `handlers/memory-triggers.ts:291-320` actively uses them to prevent cross-scope trigger leaks. The runtime validator is also aligned with the narrower surface, not the handler, in `schemas/tool-input-schemas.ts:177-183`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:14:### [P2] `memory_quick_search` returns envelopes labeled as `memory_search`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:17:**Issue** The dispatcher advertises a distinct `memory_quick_search` tool, but it forwards directly into `handleMemorySearch()` without overriding the response metadata. As a result, success and error envelopes identify the tool as `memory_search`, not the tool the caller actually invoked.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:19:**Evidence** `tools/memory-tools.ts:47-64` validates `memory_quick_search` and then returns `handleMemorySearch(quickArgs)`. `handlers/memory-search.ts:444-457` hard-codes `tool: 'memory_search'` in the cursor path, and the handler uses the same hard-coded tool name throughout the rest of the response-building branches. That makes the response surface inconsistent for clients that inspect `tool`, telemetry, or audit logs.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:41:### [P2] Dispatcher-local `ContextArgs` already drifted from the public `memory_context` contract
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:46:**Evidence** `tool-schemas.ts:43-43` includes `profile` in the published `memory_context` schema. `handlers/memory-context.ts:104-121` defines a handler-local `ContextArgs` interface that also includes `profile`. But `tools/types.ts:41-57` stops at `anchors` and omits `profile`, so the dispatcher layer's own typed contract is already stale.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-023.md:52:The most important API-surface issue is that `memory_match_triggers` has a scoped handler path that is impossible to reach through the published tool contract. After that, the main consistency problem is drift between the public JSON schema and the actual dispatcher behavior: `memory_quick_search` reports itself as the wrong tool, shared-memory admin mutations have undocumented exclusivity rules, and several numeric/string bounds exist only in the Zod layer. The dispatcher-local TypeScript arg definitions are also starting to diverge from the public schema, which increases the odds of more silent contract drift.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-002.md:58:11. **`mcp_server/lib/search/reranker.ts`** -- Simple score-based reranking utility. Separate from cross-encoder neural reranking.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-002.md:59:    [SOURCE: file header: "Simple score-based reranking utility. Sorts results by score descending"]
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-002.md:95:27. **`mcp_server/lib/search/vector-index-impl.ts`** -- Facade/redirect file noting implementation split into focused modules.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-002.md:98:28. **`mcp_server/scripts/reindex-embeddings.ts`** -- Compatibility wrapper that delegates to scripts/dist.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-017.md:10:The scan's incremental fast path trusts `categorizeFilesForIndexing()` to skip files based only on `file_mtime_ms` and embedding status. That means real content changes can be missed whenever a rewrite preserves mtime or lands within the `< 1000ms` tolerance window, even though the stored row already carries `content_hash` and the stat call already has `size`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-017.md:13:`handleMemoryIndexScan()` sends every discovered file through `incrementalIndex.categorizeFilesForIndexing(files)` and then treats `categorized.toSkip` as already up to date at `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index.ts:344-364`. In the helper, `shouldReindex()` returns `skip` whenever `Math.abs(fileInfo.mtime - stored.file_mtime_ms) < MTIME_FAST_PATH_MS` unless embedding is pending/failed at `.opencode/skills/system-spec-kit/mcp_server/lib/storage/incremental-index.ts:145-172`. The same helper reads `content_hash` from storage and `size` from `fs.statSync()`, but neither value participates in the skip decision at `.opencode/skills/system-spec-kit/mcp_server/lib/storage/incremental-index.ts:25-37` and `.opencode/skills/system-spec-kit/mcp_server/lib/storage/incremental-index.ts:91-99`.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-017.md:26:After categorization, the handler assigns `filesToDelete = categorized.toDelete` and immediately executes `deleteStaleIndexedRecords(filesToDelete)` at `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index.ts:344-370`. Only after that does it start `processBatches(filesToIndex, ...)` for the current files at `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index.ts:381-385`. `deleteStaleIndexedRecords()` calls `vectorIndex.deleteMemory(staleRecordId)` inline for each stale row at `.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index.ts:224-260`, so those deletions are committed independently of the later reindex work.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-017.md:36:The handler delegates bulk scan work to `processBatches()` without enforcing any upper bound on batch size. Because the batch processor runs each batch via `Promise.all()`, an oversized `SPEC_KIT_BATCH_SIZE` can fan out a large number of simultaneous parses/embeddings and create an avoidable OOM risk on large scans.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/handover.md:122:memory_search({ specFolder: "044-speckit-test-suite", includeContent: true })
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-02/iterations/iteration-006.md:18:| Unified graph schema across code concepts | Code Graph | L | Cross-system if shared | External Project's schema includes code, communities, processes, routes, tools, and embeddings; making that a shared Public graph would collapse Code Graph, Memory, and Skill Advisor boundaries [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/ARCHITECTURE.md:456] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/ARCHITECTURE.md:466] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:18] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_graph_compiler.py:42]. |
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-02/iterations/iteration-006.md:31:- SUPERFICIALLY PORTABLE BUT REJECT: one shared Public graph for code, memory, and skills. External Project intentionally unifies code symbols, communities, processes, routes, tools, relations, and embeddings in one graph, but Public's owners encode different truth units: Code Graph owns structural code nodes/edges, Memory owns causal memory relations, and Skill Advisor owns skill metadata edges [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/ARCHITECTURE.md:348] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/ARCHITECTURE.md:460] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-db.ts:68] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/lib/storage/causal-edges.ts:18] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_graph_compiler.py:42].
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:7:For `system-spec-kit` + Spec Kit Memory MCP, the strongest fit is Memori's explicit dual memory channels: (1) deterministic conversation replay and (2) semantic fact recall with relevance thresholding and optional lexical+dense reranking. [SOURCE: https://raw.githubusercontent.com/MemoriLabs/Memori/main/memori/llm/_base.py] [SOURCE: https://raw.githubusercontent.com/MemoriLabs/Memori/main/memori/search/_core.py]
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:14:- Recall path computes embeddings and runs fact search; selected facts are injected into system/instructions/messages by provider-specific logic.
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:34:3. Retrieve candidate facts via vector similarity + optional lexical weighting.
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:45:4. Response becomes `Memories` structure (facts, embeddings, process attributes, semantic triples).
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:54:- Semantic memory: `memori_entity_fact` (content + embedding + frequency/last_time).
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:74:- **Hybrid ranking** (dense similarity + lexical score) rather than embedding-only ranking.
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:91:- First-run performance includes embedding model setup/download overhead.
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:92:- Recall quality is threshold/embedding-limit sensitive and requires tuning.
./.opencode/specs/system-spec-kit/z_archive/020-mcp-working-memory-hybrid-rag/scratch/research-source-05-memori.md:115:- `memori/memory/recall.py` - recall query flow, embedding generation, retries, cloud/local recall parsing.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:56:- Built-in mocking capabilities for sqlite-vec, embeddings
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:108:1. **sqlite-vec** - In-memory mock for vector operations
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:109:2. **Embedding service** - Pre-computed embeddings, skip Ollama
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:117:- Pre-computed embeddings provide deterministic results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:136:| Trigger matching | <50ms | memory_match_triggers() |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:137:| Vector search | <500ms | memory_search() with vector |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:138:| Memory save | <1s | Full save with embedding |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:142:- <500ms vector search provides acceptable user experience
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/decision-record.md:282:1. **Ollama alternative**: Should we use a lighter embedding model for tests?
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-02/iterations/iteration-002.md:28:- This makes External Project schema vocabulary superficially similar but not directly portable: common relations like `CONTAINS`, `IMPORTS`, `CALLS`, `EXTENDS`, and `IMPLEMENTS` align, but External Project's Process, Route, Tool, Community, and embedding schema encode product capabilities Public has not modeled in Code Graph storage [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/src/core/lbug/schema.ts:110] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/src/core/lbug/schema.ts:127] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/src/core/lbug/schema.ts:178] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/src/core/lbug/schema.ts:190] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/lib/code-graph-db.ts:68].
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-02/iterations/iteration-002.md:43:- Defer or reject for now: full External Project schema breadth, process nodes, route nodes, tool nodes, community nodes, vector table, and broad relation list, because Public's Code Graph currently has a much smaller node and edge contract with explicit edge-type validation [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/shared/src/lbug/schema-constants.ts:11] [SOURCE: .opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/external/shared/src/lbug/schema-constants.ts:49] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/lib/indexer-types.ts:6] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/lib/indexer-types.ts:12] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/query.ts:31].
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/003-continuity-memory-runtime/002-memory-quality-remediation/research/iterations/iteration-004.md:30:- AI-provided trigger phrases and auto-extracted ones are merged in two places: first in workflow before write, then again in the indexer before vector persistence. The workflow merge is the path that contaminates saved markdown; the indexer merge can further contaminate indexed metadata because it does not re-filter manual phrases. [CITATION: `.opencode/skills/system-spec-kit/scripts/core/workflow.ts:1232-1268`, `.opencode/skills/system-spec-kit/scripts/core/memory-indexer.ts:104-137`]
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:5:### [P1] Auto-mode fallback can quietly downgrade from cloud embeddings to HF local while config introspection still reports the cloud provider
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:6:**File** `.opencode/skills/system-spec-kit/shared/embeddings/factory.ts`, `.opencode/skills/system-spec-kit/shared/embeddings/README.md`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:8:**Issue** `createEmbeddingsProvider()` automatically falls back from `voyage` or `openai` to `hf-local` whenever warmup fails or provider construction throws in auto mode, but that downgrade is only logged. The exported `getProviderInfo()` helper still reports the env-derived provider from `resolveProvider()`, not the provider actually returned after fallback. In practice that means operators can believe they are using Voyage or OpenAI while the runtime has already degraded to local 768-d embeddings with lower retrieval quality.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:15:**File** `.opencode/skills/system-spec-kit/shared/embeddings/factory.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:17:**Issue** The module exports a fail-fast `validateApiKey()` helper, but neither `getStartupEmbeddingDimension()` nor `createEmbeddingsProvider()` enforces that validation before provider selection and dimension resolution. Because of that separation, startup code can resolve a cloud provider and its embedding dimension, initialize downstream DB/profile state from that choice, and only later discover that the key is invalid or the provider is unreachable.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:19:**Evidence** `factory.ts:167-181` resolves the startup embedding dimension directly from env/provider detection. `factory.ts:249-400` creates and optionally warms a provider, but it never calls `validateApiKey()`. The validation contract is only documented as “should be called during MCP server startup” in `factory.ts:436-441`, which means the preflight is advisory rather than enforced by the embedding factory itself. If callers use the startup-dimension helper before invoking validation, the cloud provider decision has already influenced initialization.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:24:**File** `.opencode/skills/system-spec-kit/shared/embeddings/factory.ts`, `.opencode/skills/system-spec-kit/shared/embeddings/providers/openai.ts`, `.opencode/skills/system-spec-kit/shared/embeddings/providers/voyage.ts`, `.opencode/skills/system-spec-kit/shared/embeddings/providers/hf-local.ts`, `.opencode/skills/system-spec-kit/shared/embeddings/profile.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:26:**Issue** The factory accepts any positive `options.dim` and passes it into provider constructors, which then use that value as their expected embedding dimension and as part of the embedding profile/DB slug. But the actual provider requests never ask the remote model to emit that dimension, and the local model cannot change output width at all. That means non-default dimensions fail late at embedding time after the profile/database identity has already been built around an impossible schema.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:33:**File** `.opencode/skills/system-spec-kit/shared/embeddings/providers/hf-local.ts`, `.opencode/skills/system-spec-kit/shared/embeddings/providers/openai.ts`, `.opencode/skills/system-spec-kit/shared/embeddings/providers/voyage.ts`
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:35:**Issue** The local provider advertises a per-embedding timeout, but inference never wraps model execution in any timeout logic, so a slow or hung local inference can block indefinitely. On the cloud side, each request has a 30s abort, but warmup is allowed to wait through the full retry chain because there is no end-to-end warmup deadline in the provider or factory layer.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:37:**Evidence** `hf-local.ts:16-18` defines `EMBEDDING_TIMEOUT` and `MODEL_LOAD_TIMEOUT`, and `hf-local.ts:88` stores the embedding timeout on the instance, but `hf-local.ts:207-238` runs `await model(...)` without using `this.timeout`. For cloud providers, `openai.ts:16`, `openai.ts:99`, `openai.ts:116-117`, and `voyage.ts:16`, `voyage.ts:124`, `voyage.ts:141-142` only enforce per-request abort timers. Warmup then delegates to the retried request path in `openai.ts:256-270` and `voyage.ts:286-300`, so slow transient failures can consume the entire retry sequence before fallback or failure is decided.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/026-memory-database-refinement/review/iterations/iteration-028.md:43:The biggest problems are the hidden quality downgrade path and the late validation boundary: auto mode can degrade from Voyage/OpenAI to HF local without structured signaling, and the fail-fast API key check is not coupled to provider/dimension selection. I also found a concrete schema-safety bug where unchecked `dim` overrides become part of the profile/database identity even though the providers never request those dimensions, plus incomplete timeout enforcement for slow providers. I did not find a public batch-embedding surface in this directory, so I do not have a defensible per-item batch-loss finding from these files alone.
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/023-implementation-orchestration-prompt.md:155:`cli.ts`, `core/config.ts`, `handlers/index.ts`, `handlers/memory-crud-health.ts`, `handlers/shared-memory.ts`, `handlers/v-rule-bridge.ts`, `lib/cognitive/archival-manager.ts`, `lib/cognitive/tier-classifier.ts`, `lib/errors/core.ts`, `lib/eval/eval-db.ts`, `lib/ops/file-watcher.ts`, `lib/scoring/composite-scoring.ts`, `lib/search/vector-index-store.ts`, `scripts/map-ground-truth-ids.ts`, `scripts/reindex-embeddings.ts`, `startup-checks.ts`
./.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/scratch/023-implementation-orchestration-prompt.md:252:| B | `memory-index.ts` + `vector-index-store.ts` | Run index-related tests |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/comprehensive-analysis.md:76:**Description:** Setting `includeConstitutional: false` in memory_search does not exclude constitutional memories from results.
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/comprehensive-analysis.md:99:| vector-index.js | 0 | 1 | 4 | GOOD |
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/comprehensive-analysis.md:142:4. **vector-index.js**: Add path validation to getMemoryPreview
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/comprehensive-analysis.md:143:5. **context-server.js**: Add limit bounds to memory_search
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/044-speckit-test-suite/comprehensive-analysis.md:156:7. Implement parallel file reads in vectorSearchEnriched
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/015-manual-testing-per-playbook/013-memory-quality-and-indexing/plan.md:80:- **Execution layer**: Manual operator actions plus MCP calls to `memory_save`, `memory_index_scan`, `memory_search`, and quality gate pipeline functions.
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/015-manual-testing-per-playbook/013-memory-quality-and-indexing/plan.md:132:- [ ] Run 111 (deferred lexical-only indexing) -- lexical index without embedding
./.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/007-code-audit-per-feature-catalog/scratch/archive-research-2026-03-22/iteration-003.md:63:**memory_search (001-retrieval, F2)**: The audit noted "15+ source files missing from catalog" yet classified it as... ambiguous. The implementation-summary lists this under per-feature findings without explicit MATCH/PARTIAL tagging. The finding "15+ source files missing" sounds like PARTIAL or worse, yet the summary header claims "9 MATCH, 1 PARTIAL". This suggests the 15+ missing files issue may have been absorbed into a MATCH classification.
./.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/007-external-project/research/007-external-project-pt-02/iterations/iteration-003.md:34:- Public `code_graph_context` accepts natural-language input, query mode, subject, CocoIndex/manual/graph seeds, budget/profile, and trace flags; it emits readiness/trust metadata, resolved anchors with confidence/source/provider/snippet/range, graph context, text brief, metadata, and detector provenance [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:595] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts:601] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/context.ts:162] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/context.ts:232] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/context.ts:245] [SOURCE: .opencode/skills/system-spec-kit/mcp_server/code-graph/handlers/context.ts:260].
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/tests/integration.test.js:35:  vectorSearch100: 200,         // Vector search with 100 results
./.opencode/specs/system-spec-kit/z_archive/001-fix-command-dispatch/z_archive/072-speckit-template-memory-ranking-release/tests/integration.test.js:311:    it('should fuse vector and FTS results correctly', () => {
./.opencode/specs/system-spec-kit/z_archive/00on-systems/004-opencode-mnemosyne-main/research/research.md:293420:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293421:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293422:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293423:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293424:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293425:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:332:    let index: BM25Index;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293426:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:335:      index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293427:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293428:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293429:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293430:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:365:    it('T036.5: BM25 formula produces valid scores', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293431:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:383:      const idx = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293432:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293433:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293434:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:392:     T037: ENABLE_BM25 feature flag controls activation
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293435:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:395:  describe('T037: ENABLE_BM25 feature flag controls activation', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293436:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293437:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:401:      delete process.env.ENABLE_BM25;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293438:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293439:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:406:      process.env.ENABLE_BM25 = 'true';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293440:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:411:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293441:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:417:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293442:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293443:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293444:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:452:     T038: BM25 integration with hybrid search pipeline
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293445:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:455:  describe('T038: BM25 integration with hybrid search pipeline', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293453:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293454:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293457:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293458:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293463:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:498:     T039: combined_lexical_search() merges FTS5 + BM25 results
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293464:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:501:  describe('T039: combined_lexical_search() merges FTS5 + BM25', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293469:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:512:    it.skipIf(!hybridSearch)('T039.3: combinedLexicalSearch returns BM25 results', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293470:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293471:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293474:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293477:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293480:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293483:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293484:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293487:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293488:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293492:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:577:describe('C138: Weighted BM25 FTS5 Enhancements', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293493:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:578:  it('C138-T1: BM25 index exports getIndex function', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293494:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:582:  it('C138-T2: DEFAULT_K1 is standard BM25 constant', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293495:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:587:  it('C138-T3: DEFAULT_B is standard BM25 constant', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293498:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:663:    const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293499:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:675:    const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293500:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:715:    vi.doMock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293501:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:778:  it('BM25 re-index fires when triggerPhrases change', async () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293502:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:784:  it('BM25 re-index fires when title changes', async () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293503:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293504:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293505:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:819:      .toThrow('BM25 re-index failed: bad bm25 payload');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293506:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:826:  if (ORIGINAL_ENABLE_BM25 === undefined) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293507:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:827:    delete process.env.ENABLE_BM25;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293508:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-index.vitest.ts:829:    process.env.ENABLE_BM25 = ORIGINAL_ENABLE_BM25;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293510:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:54:  // Simulate vector + FTS5 + graph returning mixed results
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293516:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:164:      sourcesHit: ['vector', 'fts5', 'graph'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293519:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:204:  it('T3: pipeline hits vector, fts5, and graph sources', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293521:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-138-pipeline.vitest.ts:207:    expect(response.metrics.sourcesHit).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293537:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:23:  /** Weight for semantic (vector) search component, 0-1 */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293538:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/artifact-routing.ts:25:  /** Weight for keyword (BM25) search component, 0-1 */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293539:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293540:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:1:// TEST: BM25 SECURITY
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293541:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:5:  BM25Index,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293542:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:38:      throw new Error(`Unexpected SQL in BM25 rebuild test: ${sql}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293543:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:43:describe('BM25 Security & Coverage Gap Tests', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293544:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:298:    it('S44: Combined attack vector neutralized', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293545:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:370:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293546:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:379:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293547:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:392:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293548:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293549:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:413:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293550:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:434:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293551:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:456:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293552:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:483:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293553:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:489:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293554:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:497:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293555:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:506:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293556:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts:514:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293557:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:1:// TEST: SQLite FTS5 BM25 Search (C138-P2)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293558:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:2:// Verifies weighted BM25 scoring via FTS5 bm25() function.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293559:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:9:  FTS5_BM25_WEIGHTS,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293560:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:16:describe('C138-P2 SQLite FTS5 BM25 Search', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293561:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:79:  // ---- T2: BM25 weights are correct ----
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293562:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:80:  it('T2: FTS5_BM25_WEIGHTS has correct values', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293563:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:81:    expect(FTS5_BM25_WEIGHTS[0]).toBe(10.0); // title
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293564:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:82:    expect(FTS5_BM25_WEIGHTS[1]).toBe(5.0);  // trigger_phrases
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293565:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:83:    expect(FTS5_BM25_WEIGHTS[2]).toBe(2.0);  // file_path
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293566:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:84:    expect(FTS5_BM25_WEIGHTS[3]).toBe(1.0);  // content_text
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293567:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.ts:87:  // ---- T3: Basic BM25 search returns results ----
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293568:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:7:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293569:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:80:  vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293570:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:81:  vi.spyOn(vectorIndex, 'getDb').mockReturnValue(
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293571:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:82:    isolatedDb as unknown as NonNullable<ReturnType<typeof vectorIndex.getDb>>
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293572:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:177:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293573:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:178:        () => ({} as ReturnType<typeof vectorIndex.initializeDb>)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293574:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:180:      vi.spyOn(vectorIndex, 'getDb').mockReturnValue(
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293575:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:181:        {} as NonNullable<ReturnType<typeof vectorIndex.getDb>>
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293576:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:364:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293577:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:393:      } as unknown as NonNullable<ReturnType<typeof vectorIndex.getDb>>;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293578:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:395:      vi.spyOn(vectorIndex, 'getDb').mockReturnValue(fakeDb);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293579:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:445:        vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293580:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:446:        vi.spyOn(vectorIndex, 'getDb').mockReturnValue(
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293581:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts:447:          db as unknown as NonNullable<ReturnType<typeof vectorIndex.getDb>>
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293582:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-delete-cascade.vitest.ts:7:type VectorIndexModule = typeof import('../lib/search/vector-index');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293583:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-delete-cascade.vitest.ts:18:    mod = await import('../lib/search/vector-index');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293584:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:106:      channel: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293585:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:146:    config: { channels: ['vector', 'bm25', 'fts5'] as AblationChannel[] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293586:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:221:    it('contains vector, bm25, fts5, graph, trigger', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293587:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:222:      expect(ALL_CHANNELS).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293588:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:321:    it('disables vector channel correctly', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293589:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:322:      const flags = toHybridSearchFlags(new Set<AblationChannel>(['vector']));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293590:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:354:      const flags = toHybridSearchFlags(new Set<AblationChannel>(['vector', 'graph']));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293591:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:374:        new Set<AblationChannel>(['vector', 'bm25', 'fts5', 'graph', 'trigger']),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293592:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:437:        channels: ['vector'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293593:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:477:      // Set up channel contributions: vector provides first half, bm25 provides second half
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293594:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:480:        ['vector', relevantIds.slice(0, mid)],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293595:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:487:        channels: ['vector', 'bm25'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293596:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:547:        channels: ['vector'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293597:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:577:        if (disabledChannels.has('vector')) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293598:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:578:          throw new Error('vector channel outage');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293599:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:590:        channels: ['vector', 'bm25'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293600:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:605:        channel: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293601:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:606:        error: 'vector channel outage',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293602:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:610:        expect.stringContaining('[ablation] Channel "vector" failed'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293603:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:611:        expect.stringContaining('vector channel outage'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293604:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:650:      const channels: AblationChannel[] = ['vector', 'bm25', 'fts5'];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293605:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:728:      expect(md).toContain('| vector ');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293606:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:748:      expect(dataRows[0]).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293607:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:758:      const vectorLine = md.split('\n').find(l => l.includes('| vector'));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293608:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:759:      expect(vectorLine).toBeDefined();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293609:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:760:      expect(vectorLine).toContain('*');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293610:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:779:      const vectorLine = md.split('\n').find(l => l.includes('| vector'));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293611:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:780:      expect(vectorLine).toContain('CRITICAL');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293612:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:792:      expect(md).toContain('**vector**');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293613:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:818:            channel: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293614:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:942:    expect(channels).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293615:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:946:    // Verify vector channel delta value
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293616:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:947:    const vectorRow = deltaRows.find(r => r.channel === 'vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293617:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:948:    expect(vectorRow).toBeDefined();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293618:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:949:    expect(vectorRow!.metric_value).toBeCloseTo(-0.3);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293619:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:952:    const meta = JSON.parse(vectorRow!.metadata);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293620:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:983:        { channel: 'vector', error: 'vector outage', queryId: 1, query: 'q1' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293621:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1059:    // Ablating vector should show a measurable negative delta.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293622:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1079:    // Build a search function where vector uniquely contributes some results
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293623:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1095:      // When vector is disabled, only return the second half of relevant IDs
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293624:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1096:      // This simulates vector contributing the first half uniquely
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293625:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1098:      if (disabledChannels.has('vector')) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293626:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1113:      channels: ['vector', 'bm25'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293627:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1133:    // Specifically, vector should show negative delta (removing it hurts)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293628:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1134:    const vectorResult = report.results.find(r => r.channel === 'vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293629:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1135:    expect(vectorResult).toBeDefined();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293630:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1136:    expect(vectorResult!.delta).toBeLessThan(0);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293631:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1146:    expect(md).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293632:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1171:      ['vector', relevantIds.slice(0, third)],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293633:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1179:      channels: ['vector', 'bm25', 'fts5'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293634:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1194:    for (const channel of ['vector', 'bm25', 'fts5']) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293635:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1249:    expect(md).toContain('| vector ');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293636:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1289:      // Verify multi-metric rows exist for vector
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293637:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1290:      const vectorMetricRows = rows.filter(
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293638:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1291:        r => r.channel === 'vector' && r.metric_name.startsWith('ablation_') && r.metric_name !== 'ablation_recall@20_delta' && r.metric_name !== 'ablation_baseline_recall@20',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293639:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1293:      expect(vectorMetricRows.length).toBe(8);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293640:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1296:      const metricNames = vectorMetricRows.map(r => r.metric_name);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293641:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1330:        if (disabled.has('vector')) ids = ids.slice(Math.ceil(ids.length / 2));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293642:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1335:        channels: ['vector'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293643:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/ablation-framework.vitest.ts:1373:        channels: ['vector'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293644:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/eval/eval-logger.ts:93:  /** Channel name: "vector", "bm25", "graph", or "trigger". */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293645:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:5:// Weighted BM25 scoring for FTS5 full-text search.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293647:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:9:import { BM25_FTS5_WEIGHTS, normalizeLexicalQueryTokens } from './bm25-index.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293648:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:147: * Execute a weighted BM25 FTS5 search against memory_fts.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293649:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:156: * @returns Array of results with BM25 scores (higher = better)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293650:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:195:  const [w0, w1, w2, w3] = BM25_FTS5_WEIGHTS;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293651:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:252:    console.warn(`[sqlite-fts] BM25 FTS5 search failed: ${msg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293652:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:281:  BM25_FTS5_WEIGHTS as FTS5_BM25_WEIGHTS,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293653:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/sqlite-fts.ts:291: * BM25 FTS result and option types exposed by the SQLite FTS module.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293655:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:45:    source: 'lib/search/vector-index-store.ts',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293656:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:50:    source: 'lib/search/vector-index-store.ts',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293657:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-flag-reference-docs.vitest.ts:60:    source: 'lib/search/vector-index-store.ts',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293658:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints-edge.vitest.ts:4:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293659:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints-edge.vitest.ts:92:      vectorIndex,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293660:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints-edge.vitest.ts:95:    const db = vectorIndex.initializeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293661:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints-edge.vitest.ts:100:    vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293662:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-checkpoints-edge.vitest.ts:211:    const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293663:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/trigger-matcher.vitest.ts:32:// without better-sqlite3 or vector-index wiring.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293664:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/trigger-matcher.vitest.ts:33:vi.mock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293665:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:27:        '../lib/search/vector-index-schema.ts'
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293666:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:42:        '../lib/search/vector-index-schema.ts'
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293667:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:56:        '../lib/search/vector-index-schema.ts'
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293668:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:225:      // The vectorSearchFn call must use 2 * maxRelated, not maxRelated + 1
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293669:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:230:    it('BM25 search respects the limit parameter', async () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293670:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:231:      const { BM25Index } = await import('../lib/search/bm25-index');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293671:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:233:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293672:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:245:    it('BM25 search with limit=0 returns empty array', async () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293673:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:246:      const { BM25Index } = await import('../lib/search/bm25-index');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293674:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/regression-suite.vitest.ts:248:      const index = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293680:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-search-fn.ts:152: * Scores incorporate both edge strength and FTS5 BM25 relevance.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293681:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293684:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:103:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293685:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:107:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293686:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:125:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293687:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:128:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293688:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:145:      makeFused('a1', 0.95, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293689:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:147:      makeFused('a2', 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293690:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:149:      makeFused('a3', 0.75, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293691:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:152:      ['vector', [makeChannel('a1', 0.95), makeChannel('a2', 0.85), makeChannel('a3', 0.75)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293692:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:171:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293693:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:174:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293694:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:175:      ['bm25',   [makeChannel('b1', 0.65, { title: 'BM25 Doc' })]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293695:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:186:    expect((promoted as Record<string, unknown>)?.title).toBe('BM25 Doc');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293696:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:192:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293697:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:198:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293698:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:229:      makeFused('a1', 0.95, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293699:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:232:      makeFused('a2', 0.72, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293700:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:235:      ['vector', [makeChannel('a1', 0.95), makeChannel('a2', 0.72)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293701:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:252:      makeFused('a1', 0.95, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293702:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:254:      makeFused('a2', 0.78, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293703:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:258:      ['vector', [makeChannel('a1', 0.95), makeChannel('a2', 0.78)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293704:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:279:      makeFused('a1', 0.93, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293705:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:281:      makeFused('a2', 0.81, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293706:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:285:      ['vector', [makeChannel('a1', 0.93), makeChannel('a2', 0.81)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293707:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:302:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293708:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:305:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293709:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:323:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293710:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:326:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293711:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:357:      makeFused('a1', 0.92, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293712:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:359:      makeFused('a2', 0.79, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293713:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:362:      ['vector', [makeChannel('a1', 0.92), makeChannel('a2', 0.79)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293714:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:382:      ['vector', [makeChannel('a1', 0.8)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293715:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:395:    const fused: FusedResult[] = [makeFused('a1', 0.8, 'vector')];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293716:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:397:      ['vector', [makeChannel('a1', 0.8)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293717:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:410:      makeFused('a1', 0.8, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293718:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:413:      ['vector', []],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293719:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:427:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293720:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:431:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293721:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:447:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293722:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:451:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293723:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:467:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293724:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:470:      ['vector', [makeChannel('a1', 0.9)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293725:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:486:      makeFused('a1', 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293726:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:487:      makeFused('a2', 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293727:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:491:      ['vector', [makeChannel('a1', 0.9), makeChannel('a2', 0.85)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293728:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:498:    expect(result.enforcement.channelCounts['vector']).toBe(2);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293729:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:515:      makeFused('a1', 0.95, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293730:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:517:      makeFused('a2', 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293731:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/channel-enforcement.vitest.ts:521:      ['vector', [makeChannel('a1', 0.95), makeChannel('a2', 0.85)]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293732:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/chunking/anchor-chunker.ts:63:/** Max characters for parent summary (BM25 fallback) */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293733:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-health-edge.vitest.ts:4:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293734:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-health-edge.vitest.ts:23:  vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293735:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-health-edge.vitest.ts:24:  vectorIndex.initializeDb(':memory:');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293736:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-health-edge.vitest.ts:28:  vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293737:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/trigger-config-extended.vitest.ts:17:   MODULE LOADING  (mock vector-index for trigger-matcher)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293738:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/trigger-config-extended.vitest.ts:104:vi.mock('../lib/search/vector-index.js', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293739:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:8:// TEST: VECTOR INDEX IMPLEMENTATION (vector-index-impl)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293740:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:9:// Core vector search implementation — pure functions, DB ops,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293741:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:11:// DB-dependent (uses better-sqlite3 + sqlite-vec).
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293742:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:12:type VectorIndexModule = typeof import('../lib/search/vector-index-impl');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293743:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:15:type VectorSearchResult = ReturnType<VectorIndexModule['vectorSearch']>[number];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293744:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:43:      mod = await import('../lib/search/vector-index-impl');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293745:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:87:        'vectorSearch', 'getConstitutionalMemories',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293746:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:91:        'vectorSearchEnriched', 'multiConceptSearchEnriched',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293747:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:242:      const tags = mod.extractTags('---\ntags: [memory, search, "vector"]\n---\n\nContent');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293748:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:245:      expect(tags).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293749:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:857:      vi.doMock('../lib/search/vector-index-store', async (importOriginal) => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293750:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:858:        const actual = await importOriginal<typeof import('../lib/search/vector-index-store')>();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293751:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:865:      const mutations = await import('../lib/search/vector-index-mutations');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293752:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1064:  describe('Vector Search (sqlite-vec dependent)', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293753:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1122:    let vectorMod!: VectorIndexModule;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293754:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1123:    let vectorTmpDir: string | null = null;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293755:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1129:        vectorMod = mod;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293756:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1133:      vectorTmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'vec-idx-mock-'));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293757:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1134:      const vectorDbPath = path.join(vectorTmpDir, 'test-context-index.sqlite');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293758:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1138:      process.env.MEMORY_DB_PATH = vectorDbPath;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293759:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1139:      process.env.MEMORY_ALLOWED_PATHS = vectorTmpDir;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293760:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1142:      vi.doMock('../lib/search/vector-index-store', async (importOriginal) => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293761:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1143:        const actual = await importOriginal<typeof import('../lib/search/vector-index-store')>();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293762:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1148:          is_vector_search_available: () => true,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293763:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1152:      vectorMod = await import('../lib/search/vector-index-impl');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293764:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1153:      const db = vectorMod.initializeDb(vectorDbPath);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293765:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1168:      `).run(String(vectorMod.getEmbeddingDim()));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293766:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1175:          vectorMod?.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293767:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1177:        vi.doUnmock('../lib/search/vector-index-store');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293768:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1193:      if (vectorTmpDir && fs.existsSync(vectorTmpDir)) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293769:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1194:        fs.rmSync(vectorTmpDir, { recursive: true, force: true });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293770:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1198:    it('indexMemory creates vector memory with embedding', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293771:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1199:      vecMemId = vectorMod.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293772:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1203:        triggerPhrases: ['vector', 'search'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293773:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1208:      const mem = vectorMod.getMemory(vecMemId);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293774:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1212:    it('indexMemory creates additional vector memories for search', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293775:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1213:      vectorMod.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293776:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1221:      vectorMod.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293777:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1233:      const idA = vectorMod.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293778:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1242:      const idB = vectorMod.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293779:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1251:      const db = vectorMod.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293780:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1259:      vectorMod.updateMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293781:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1270:    it('vectorSearch returns results', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293782:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1272:      const searchResults = vectorMod.vectorSearch(query, { limit: 5 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293783:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1281:    it('vectorSearch filters by specFolder', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293784:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1283:      const filtered = vectorMod.vectorSearch(query, { limit: 10, specFolder: 'specs/test-vec' });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293785:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1287:    it('vectorSearch respects minSimilarity', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293786:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1289:      const strict = vectorMod.vectorSearch(query, { limit: 10, minSimilarity: 99 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293787:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1297:        vectorMod.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293788:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1308:        vectorMod.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293789:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1320:      const mcResults = vectorMod.multiConceptSearch([emb1, emb2], { limit: 5 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293790:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1326:        vectorMod.multiConceptSearch([makeEmbedding(1)], { limit: 5 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293791:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1333:      const updatedId = vectorMod.updateMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293792:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1339:      const mem = vectorMod.getMemory(vecMemId!);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293793:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1349:    it('vectorSearchEnriched — exported and falls back to keyword search without embedding', async () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293794:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1350:      expect(typeof mod.vectorSearchEnriched).toBe('function');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293795:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1352:      const results = await mod.vectorSearchEnriched('test query', 5);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293796:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1392:      const result = mod.learnFromSelection('vector search implementation testing', deferredId1!);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293797:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1395:      // "vector", "search", "implementation" should be added (each >= 4 chars, not stop words)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293798:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1396:      expect(mem?.trigger_phrases).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293799:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1417:      const result = mod.learnFromSelection('alpha vector search', deferredId1!);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293800:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1418:      // "alpha", "vector", "search" already exist — no new terms
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293803:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293804:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunk-thinning.vitest.ts:351:    const vectorIndex = await import('../lib/search/vector-index');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293805:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunk-thinning.vitest.ts:357:    try { vectorIndex.closeDb(); } catch { /* ignore */ }
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293806:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunk-thinning.vitest.ts:358:    vectorIndex.initializeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293807:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunk-thinning.vitest.ts:399:      const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293808:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunk-thinning.vitest.ts:408:      vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293812:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:191:      source: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293814:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:223:    expect(item2!.sources).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293824:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:381:    // The vector-only item should score higher than keyword-only item
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293825:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:383:      { id: 'only-vec', title: 'vector only result' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293827:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:398:    // So vector-only result should have higher RRF score
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293831:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/intent-weighting.vitest.ts:436:      source: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293839:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:41:      { source: 'vector', results: [{ id: 1 }, { id: 2 }, { id: 3 }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293840:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:58:      { source: 'vector', results: [{ id: 1 }, { id: 2 }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293842:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:81:      [{ source: 'vector', results: [{ id: 1 }, { id: 2 }] }],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293843:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:101:      { source: 'vector', results: [{ id: 1 }, { id: 2 }, { id: 3 }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293844:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:220:      source: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293845:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:243:      { id: 1, score: 0.9, source: 'vector', title: 'Short result A' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293847:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:265:      { source: 'vector', results: [{ id: 1 }, { id: 2 }, { id: 3 }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293850:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:302:      { source: 'vector', results: [{ id: 1 }, { id: 2 }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293851:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:326:      { id: 1, rrfScore: 0.02, sources: ['vector'], sourceScores: {}, convergenceBonus: 0 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293852:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:342:      source: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293853:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts:352:      { id: 1, score: 0.9, source: 'vector', title: 'Exact fit A' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293854:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:30:      { id: 101, score: 0.91, source: 'vector', sources: ['vector', 'bm25'] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293856:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:127:    const vectorPayload = byChannel.get('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293857:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:130:    expect(vectorPayload).toBeDefined();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293858:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.ts:133:    expect(vectorPayload!.resultMemoryIds).toEqual([101]);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293862:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/trigger-extractor.vitest.ts:182:      embedding vectors. The [trigger-extractor](./trigger-extractor.ts) module
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293863:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/trigger-extractor.vitest.ts:194:      - Embedding provider chain for vector generation
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293864:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:4:// Feature catalog: BM25 trigger phrase re-index gate
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293865:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:6:import { normalizeContentForBM25 } from '../parsing/content-normalizer.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293866:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:12:interface BM25SearchResult {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293867:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:15:   * BM25 term-frequency relevance score (unbounded, typically 0-25+).
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293868:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:16:   * Higher = better lexical match. Not directly comparable to vector similarity
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293870:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:22:interface BM25Stats {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293871:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:28:interface BM25DocumentSource {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293872:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:41:const BM25_WARMUP_BATCH_SIZE = 250;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293873:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293874:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:43:const BM25_DISABLED_VALUES = new Set(['0', 'false', 'no', 'off']);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293875:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:46: * C138: Field weight multipliers for weighted BM25 scoring.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293876:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293877:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293878:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:61:const BM25_FIELD_WEIGHTS: Record<string, number> = {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293879:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:62:  title: BM25_FTS5_WEIGHTS[0],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293880:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:63:  trigger_phrases: BM25_FTS5_WEIGHTS[1],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293881:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:64:  content_generic: BM25_FTS5_WEIGHTS[2],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293882:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:65:  body: BM25_FTS5_WEIGHTS[3],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293883:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:69: * Check whether the in-memory BM25 index is enabled.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293884:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293885:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:80:  const value = process.env.ENABLE_BM25?.trim().toLowerCase();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293886:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:82:  if (BM25_DISABLED_VALUES.has(value)) return false;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293887:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:83:  return BM25_ENABLED_VALUES.has(value);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293888:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293889:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:146: * Tokenize raw text into normalized BM25 terms.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293890:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:163: * Count token frequency occurrences for BM25 scoring.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293891:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:181:function normalizeTriggerPhrasesForBM25(triggerPhrases: string | string[] | null | undefined): string {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293892:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:211:function buildBm25DocumentText(row: BM25DocumentSource): string {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293893:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:219:    textParts.push(normalizeContentForBM25(row.content_text));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293894:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:222:  const triggerPhrases = normalizeTriggerPhrasesForBM25(row.trigger_phrases);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293895:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:235:// 3. BM25 INDEX CLASS
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293896:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:238:class BM25Index {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293897:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293898:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:326:    const results: BM25SearchResult[] = [];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293899:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:340:  getStats(): BM25Stats {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293900:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:415:      console.warn(`[bm25-index] Failed to sync BM25 rows: ${msg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293901:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:446:        const batchIds = pendingIds.splice(0, BM25_WARMUP_BATCH_SIZE);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293902:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:465:      console.warn(`[bm25-index] Failed to schedule BM25 warmup: ${msg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293903:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:483:let indexInstance: BM25Index | null = null;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293904:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:486: * Retrieve the shared in-memory BM25 index singleton.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293905:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:488: * @returns The process-wide {@link BM25Index} instance.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293906:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:495:function getIndex(): BM25Index {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293907:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:497:    indexInstance = new BM25Index();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293908:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:503: * Reset the shared BM25 index singleton.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293909:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:523: * entry point — both FTS5 query construction and BM25 callers should
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293910:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:533: * sanitizeQueryTokens('title:memory AND vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293911:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:534: * // ['title', 'memory', 'vector']
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293912:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:604:  BM25Index,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293913:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:617:  BM25_FTS5_WEIGHTS,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293914:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:618:  BM25_FIELD_WEIGHTS,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293915:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:622:  BM25SearchResult,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293916:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:623:  BM25Stats,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293917:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/bm25-index.ts:624:  BM25DocumentSource,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293918:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:6:// DB-dependent barrel checks use mocked vector-index imports so we can validate
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293919:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/modularization.vitest.ts:47:vi.mock('../lib/search/vector-index.js', () => mockedDbDeps);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293921:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/hydra-spec-pack-consistency.vitest.ts:28:  'mcp_server/lib/search/vector-index-mutations.ts',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293930:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-integration.vitest.ts:28:// Mock the BM25 index so no filesystem reads are attempted.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293968:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:19://     "channelContribution": { "vector": 0.44, "fts": 0.12, "graph": 0.06 }
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293969:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:45:  vector: number;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293970:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:232: * distribute the effective score across vector, fts, and graph channels.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293971:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:240:  const vectorScore = typeof row.vectorScore === 'number' && Number.isFinite(row.vectorScore)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293972:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:241:    ? Math.max(0, Math.min(1, row.vectorScore))
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293973:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:254:  if (vectorScore !== null && ftsScore !== null) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293974:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:258:      vector: Math.round(vectorScore * 100) / 100,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293975:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:275:      vector: Math.round(remaining * 0.75 * 100) / 100,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293976:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:283:      vector: Math.round(effectiveScore * 0.78 * 100) / 100,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293977:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:292:      vector: Math.round((effectiveScore - graphShare) * 100) / 100,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293978:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/result-explainability.ts:299:  return { vector: Math.round(effectiveScore * 100) / 100, fts: 0, graph: 0 };
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293979:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:332:          channel: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293980:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:347:        { eval_run_id: 1, query_id: 1, channel: 'vector', hit_count: 5, latency_ms: 12.5 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293981:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:348:        { eval_run_id: 1, query_id: 2, channel: 'vector', hit_count: 3, latency_ms: 15.0 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293982:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:360:      expect(channels).toHaveProperty('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293983:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:364:      expect(channels['vector'].queryCount).toBe(2);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293984:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:365:      expect(channels['vector'].hitCount).toBe(8);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293985:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:366:      expect(channels['vector'].avgLatencyMs).toBeCloseTo(13.75, 1);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293986:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:386:        { eval_run_id: 2, query_id: 1, channel: 'vector', hit_count: 4, latency_ms: 100.0 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293987:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:390:      const vector = report.sprints[0].channels['vector'];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293988:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:392:      expect(vector.queryCount).toBe(3);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293989:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:393:      expect(vector.hitCount).toBe(12);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293990:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:394:      expect(vector.avgLatencyMs).toBeCloseTo((12.5 + 15.0 + 100.0) / 3, 4);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293991:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:412:      expect(sprint.channelMetrics['ndcg@5']['vector'].latest).toBe(0.85);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293992:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:602:          channel: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293993:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:608:        { eval_run_id: 1, query_id: 1, channel: 'vector', hit_count: 5, latency_ms: 10.0 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293994:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:616:      expect(text).toContain('ndcg@5 [vector]');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293995:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:617:      expect(text).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293996:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:878:        { eval_run_id: 1, query_id: 1, channel: 'vector', hit_count: 5, latency_ms: 10.0 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293997:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:883:      const report = await generateDashboardReport({ channelFilter: ['vector', 'bm25'] });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:293998:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/reporting-dashboard.vitest.ts:886:      expect(channelNames).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294004:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/embedding-weighting.vitest.ts:20:    const vector = new Float32Array(vocabulary.length);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294005:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/embedding-weighting.vitest.ts:24:        vector[index] += 1;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294006:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/embedding-weighting.vitest.ts:27:    return vector;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294009:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:126:            vector: [1],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294010:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:169:            vector: [1],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294011:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:195:            vector: [1],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294012:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:332:            vector: [1],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294013:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/result-confidence-scoring.vitest.ts:371:            vector: [2],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294016:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/consolidation.ts:185: * Heuristic-only contradiction scan when vector similarity is unavailable.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294017:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/consolidation.ts:208:  // Same 5-second timeout guard as the vector-based scan to prevent
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294020:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:115:      expect(padded).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294021:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:127:      expect(DEFAULT_ROUTING_CONFIG.simple).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294022:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:139:      // Simulate simple tier: only vector and fts channels
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294023:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:140:      const channels: ChannelName[] = ['vector', 'fts'];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294024:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:142:      // Top-K results only from vector (fts missing)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294025:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:144:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294026:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:145:        makeFused(2, 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294027:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:146:        makeFused(3, 0.80, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294028:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:151:      channelResults.set('vector', [
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294029:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:175:      // Moderate tier: vector, fts, bm25
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294030:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:177:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294031:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:178:        makeFused(2, 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294032:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:179:        makeFused(3, 0.80, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294033:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:183:      channelResults.set('vector', [
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294034:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:212:        makeFused(1, 0.95, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294035:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:213:        makeFused(2, 0.90, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294036:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:218:      channelResults.set('vector', [
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294037:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:248:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294038:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:249:        makeFused(2, 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294039:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:252:      channelResults.set('vector', [makeChannelResult(1, 0.9)]);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294040:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:266:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294041:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:267:        makeFused(2, 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294042:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:270:      channelResults.set('vector', [makeChannelResult(1, 0.9), makeChannelResult(2, 0.85)]);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294043:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:288:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294044:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:289:        makeFused(2, 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294045:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:293:      channelResults.set('vector', [makeChannelResult(1, 0.9), makeChannelResult(2, 0.85)]);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294046:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:313:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294047:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:317:      channelResults.set('vector', [makeChannelResult(1, 0.9)]);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294048:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:339:      expect(route.channels).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294049:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:345:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294050:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:346:        makeFused(2, 0.85, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294051:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:347:        makeFused(3, 0.80, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294052:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:352:      channelResults.set('vector', [
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294053:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:370:      expect(sources.has('vector')).toBe(true);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294055:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:385:        makeFused(1, 0.95, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294056:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:386:        makeFused(2, 0.90, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294057:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:392:      channelResults.set('vector', [makeChannelResult(1, 0.95), makeChannelResult(2, 0.90)]);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294058:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:417:      // Fused results only from vector
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294059:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:419:        makeFused(1, 0.9, 'vector'),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294060:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/query-router-channel-interaction.vitest.ts:423:      channelResults.set('vector', [makeChannelResult(1, 0.9)]);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294061:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294062:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294063:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-eval-channels.vitest.ts:76:vi.mock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294066:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store-remediation.vitest.ts:15:} from '../lib/search/vector-index-store';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294067:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store-remediation.vitest.ts:16:import { getMemoriesByFolder, indexMemoryDeferred } from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294068:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store-remediation.vitest.ts:48:describe('vector-index-store remediation regressions', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294069:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:62:    source: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294070:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:63:    sources: ['vector', 'fts'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294071:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:71:        vector: [101],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294075:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:115:                channel: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294076:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:116:                channels: ['vector', 'fts'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294077:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/mcp-response-envelope.vitest.ts:162:    expect(result.trace?.channelsUsed).toEqual(expect.arrayContaining(['vector', 'fts']));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294079:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:9:import { IVectorStore } from '../lib/interfaces/vector-store';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294080:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/pipeline-architecture-remediation.vitest.ts:10:import { SQLiteVectorStore } from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294081:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/learned-combiner.vitest.ts:268:      // Add a 9th example (zero vector) to anchor the bias
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294082:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/learned-combiner.vitest.ts:280:      // Verify bias is close to the zero-vector label
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294083:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:5:// Split from vector-index-store.ts — contains LRUCache, query caching,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294084:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:13:} from './vector-index-types.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294085:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:17:} from './vector-index-store.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294086:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:19:  vector_search,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294087:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:20:  vector_search_enriched,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294088:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:24:} from './vector-index-queries.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294089:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:199:// Cached version of vector_search_enriched with LRU cache
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294090:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:219:  const results = await vector_search_enriched(query, limit, options);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294091:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:276:    console.warn(`[vector-index] learn_from_selection query error: ${get_error_message(e)}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294092:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:318:    console.warn(`[vector-index] learn_from_selection update error: ${get_error_message(e)}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294093:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:342:      console.warn(`[vector-index] Could not generate embedding for memory ${new_memory_id}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294094:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:346:    const similar = vector_search(embedding, {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294095:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:365:    console.warn(`[vector-index] Failed to link related memories for ${new_memory_id}: ${get_error_message(error)}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294096:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:389:    console.warn(`[vector-index] Failed to record access for memory ${memory_id}: ${get_error_message(error)}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294097:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-aliases.ts:415:  const results = await vector_search_enriched(query, fetch_limit, {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294098:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294103:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:302:      [{ id: 42, score: 0.12, source: 'vector' } as HybridSearchResult],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294104:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:312:      { id: 1, score: 0.03, source: 'vector' } as HybridSearchResult,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294105:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:319:      { id: 1, score: 0.01, source: 'vector' } as HybridSearchResult,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294106:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:329:    const existing = [{ id: 1, score: 0.13, source: 'vector' } as HybridSearchResult];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294107:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/search-fallback-tiered.vitest.ts:362:      source: 'vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294108:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/checkpoints.ts:205:  vectors?: SnapshotVectorRow[];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294109:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/checkpoints.ts:853:  if (Array.isArray(snapshot.vectors)) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294110:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/checkpoints.ts:856:      rows: snapshot.vectors.map((row) => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294111:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/checkpoints.ts:1452:      const vectorRows = tables.vec_memories?.rows ?? [];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294112:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/checkpoints.ts:1455:      const vectors = vectorRows.map((row) => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294113:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/checkpoints.ts:1465:        vectors,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294114:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/checkpoints.ts:1492:          vectorCount: vectors.length,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294115:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/checkpoint-completeness.vitest.ts:8:import { createSchema, ensureSchemaVersion } from '../lib/search/vector-index-schema';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294125:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-context.vitest.ts:610:                      channelsUsed: ['vector'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294126:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:112:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'shared', title: 'S' }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294127:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:122:      { source: SOURCE_TYPES.BM25,    results: [{ id: 'shared', title: 'S' }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294128:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:163:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'x', title: 'X' }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294129:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:176:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'y', title: 'Y' }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294130:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:186:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'z', title: 'Z' }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294131:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294132:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294133:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294134:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:238:      { source: SOURCE_TYPES.BM25, results: [
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294135:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:252:      { source: SOURCE_TYPES.BM25,    results: [{ id: 'mega', title: 'M' }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294136:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/calibrated-overlap-bonus.vitest.ts:275:      { source: SOURCE_TYPES.BM25,   results: [{ id: 'bc', title: 'BC' }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294137:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294138:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:12:import { ensureLineageTables } from '../search/vector-index-schema.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294139:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:13:import { get_embedding_dim, refresh_interference_scores_for_folder, sqlite_vec_available } from '../search/vector-index-store.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294140:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:14:import { to_embedding_buffer } from '../search/vector-index-types.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294141:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/lineage-state.ts:533:      logger.warn(`BM25 index update failed for memory ${memoryId}: ${error instanceof Error ? error.message : String(error)}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294142:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:114: * The vector + fts channels are considered "core" and always return
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294143:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:261:    const ch2 = simulatedLatencyMs(['vector', 'fts']);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294144:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:262:    const ch3 = simulatedLatencyMs(['vector', 'fts', 'bm25']);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294145:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:295:    // Simple uses vector + fts (subset of full pipeline)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294146:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/shadow-comparison.vitest.ts:365:        expect(result.channels).toEqual(['vector', 'fts', 'bm25', 'graph', 'degree']);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294149:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294150:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/governance/scope-governance.ts:8:import { ensureGovernanceTables, ensureSharedSpaceTables } from '../search/vector-index-schema.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294151:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/eval-db.vitest.ts:235:      `).run(1, 1, 'vector', 3);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294152:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/eval-db.vitest.ts:277:      `).run(1, 'mrr@5', 0.72, 'vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294153:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:130:  it('T003-02: vector-dominated results get padded with under-represented channels', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294154:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:132:      { id: 1, score: 0.9, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294155:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:133:      { id: 2, score: 0.85, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294156:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:134:      { id: 3, score: 0.8, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294157:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:138:      ['vector', [{ id: 1, score: 0.9 }, { id: 2, score: 0.85 }, { id: 3, score: 0.8 }]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294158:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:153:      { id: 1, score: 0.9, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294159:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:159:      ['vector', [{ id: 1, score: 0.9 }]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294160:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:173:      { id: 1, score: 0.9, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294161:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:177:      ['vector', [{ id: 1, score: 0.9 }]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294162:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:192:      { id: 1, score: 0.9, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294163:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-query-intelligence.vitest.ts:195:      ['vector', [{ id: 1, score: 0.9 }]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294164:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/retry-manager-health.vitest.ts:13:    vi.doMock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294165:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:20:import { clear_search_cache } from '../search/vector-index-aliases.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294166:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:21:import { refresh_interference_scores_for_folder } from '../search/vector-index-store.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294167:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:23:import { delete_memory_from_database } from '../search/vector-index-mutations.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294168:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:154: * @param embedding - The embedding vector to compare against
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294169:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:365:          console.warn('[reconsolidation] Failed to update BM25 index for merge:', message);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294170:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:401:          `BM25 repair failed after reconsolidation merge for memory ${newId}: ${repairResult.error}`;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294171:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts:754:    console.warn('[reconsolidation] Immediate BM25 repair failed:', message);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294173:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294178:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294179:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feature-eval-graph-signals.vitest.ts:322:    expect(result.sources).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294182:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/folder-relevance.vitest.ts:422:        makeResult(1, 0.9, { title: 'Memory One', source: 'vector', customField: 42 }),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294183:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/folder-relevance.vitest.ts:434:      expect((enriched[0] as Record<string, unknown>).source).toBe('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294185:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:6:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294187:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/integration-search-pipeline.vitest.ts:51:        { name: 'vectorIndex', ref: vectorIndex },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294188:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/collab/shared-spaces.ts:11:} from '../search/vector-index-schema.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294190:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:74:      'We evaluated BM25, vector search, and hybrid approaches. The hybrid',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294192:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:350:      'independently. The retrieval stage handles both BM25 and vector',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294194:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:408:    const vectorIndex = await import('../lib/search/vector-index');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294195:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:409:    vectorIndex.initializeDb(dbPath);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294196:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:410:    const embeddingDim = vectorIndex.getEmbeddingDim();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294197:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:412:    const memoryId = vectorIndex.indexMemory({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294198:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:423:    const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294199:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:428:    vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294200:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:439:    const vectorIndex = await import('../lib/search/vector-index');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294201:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:440:    vectorIndex.initializeDb(dbPath);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294202:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:442:    const memoryId = vectorIndex.indexMemoryDeferred({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294203:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:453:    const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294204:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/encoding-intent.vitest.ts:458:    vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294205:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-pipeline-enforcement.vitest.ts:7:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294206:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-pipeline-enforcement.vitest.ts:278:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294207:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-pipeline-enforcement.vitest.ts:300:    vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294208:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-pipeline-enforcement.vitest.ts:304:  vectorIndex.initializeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294209:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-save-pipeline-enforcement.vitest.ts:321:    vectorIndex.closeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294210:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:5:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294211:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:104:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294212:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:105:      vi.spyOn(vectorIndex, 'getDb').mockReturnValue({} as ReturnType<typeof vectorIndex.getDb>);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294213:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:145:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294214:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:146:      vi.spyOn(vectorIndex, 'getDb').mockReturnValue({} as ReturnType<typeof vectorIndex.getDb>);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294215:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:213:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294216:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:214:      vi.spyOn(vectorIndex, 'getDb').mockReturnValue({} as ReturnType<typeof vectorIndex.getDb>);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294217:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:310:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294218:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:311:      vi.spyOn(vectorIndex, 'getDb').mockReturnValue({} as ReturnType<typeof vectorIndex.getDb>);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294219:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:329:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294220:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:330:      vi.spyOn(vectorIndex, 'getDb').mockImplementation(() => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294221:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:344:      vi.spyOn(vectorIndex, 'initializeDb').mockImplementation(() => undefined);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294222:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts:345:      vi.spyOn(vectorIndex, 'getDb').mockReturnValue({} as ReturnType<typeof vectorIndex.getDb>);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294223:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/handler-memory-index-cooldown.vitest.ts:90:vi.mock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294224:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:2:// 1. TEST — BM25 BASELINE
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294225:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:13:// T008.8  — runBM25Baseline: runs with mocked search function
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294226:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:14:// T008.9  — runBM25Baseline: respects queryLimit config option
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294227:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:15:// T008.10 — runBM25Baseline: skipHardNegatives reduces query count
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294228:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:16:// T008.11 — runBM25Baseline: returns well-structured BM25BaselineResult
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294229:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:17:// T008.12 — runBM25Baseline: disables non-BM25 channels (only calls searchFn)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294230:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:40:  runBM25Baseline,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294231:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:41:  type BM25BaselineResult,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294232:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:42:  type BM25SearchResult,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294233:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:77:function makeMockSearchFn(count: number = 5): (query: string, limit: number) => BM25SearchResult[] {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294234:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294235:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:89:function makeMockResult(mrr5: number): BM25BaselineResult {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294236:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:107:describe('T008: BM25 Contingency Decision Matrix', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294237:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:163:describe('T008: BM25 Relative Contingency Decision', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294238:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:166:    // BM25=0.72, hybrid=0.80 → ratio=0.90 → PAUSE
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294240:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:176:    // BM25=0.40, hybrid=0.70 → ratio=0.571 → RATIONALIZE
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294241:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:184:    // BM25=0.20, hybrid=0.75 → ratio=0.267 → PROCEED
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294242:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:193:    // BM25=0.40, hybrid=0.50 → ratio=0.80 exactly
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294243:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:200:    // BM25=0.25, hybrid=0.50 → ratio=0.50 exactly
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294246:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:387:   TESTS: runBM25Baseline
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294247:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:390:describe('T008: runBM25Baseline — Runner Integration', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294248:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:394:    const result = await runBM25Baseline(mockSearch, { queryLimit: 10 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294249:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:410:    const result = await runBM25Baseline(mockSearch, { queryLimit: 7 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294250:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:420:    const withHardNeg = await runBM25Baseline(mockSearch, { skipHardNegatives: false });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294251:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:421:    const withoutHardNeg = await runBM25Baseline(mockSearch, { skipHardNegatives: true });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294252:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294253:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:430:    const result = await runBM25Baseline(mockSearch, { queryLimit: 5 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294254:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294255:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:445:    const trackingSearch = (query: string, limit: number): BM25SearchResult[] => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294256:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:450:    const result = await runBM25Baseline(trackingSearch, { queryLimit: 3 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294257:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:462:    const result = await runBM25Baseline(mockSearch, { queryLimit: 3 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294258:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:477:    const mockSearch = (query: string, _limit: number): BM25SearchResult[] => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294259:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:489:    const baseline = await runBM25Baseline(mockSearch, { queryLimit: 3 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294260:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/bm25-baseline.vitest.ts:490:    const withKOverride = await runBM25Baseline(mockSearch, { queryLimit: 3, k: 1 });
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294261:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:28:vi.mock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294262:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:103:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294263:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:226:  vi.mocked(vectorIndex.indexMemory).mockImplementation((params) => insertIndexedRow(params, 'success'));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294264:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:227:  vi.mocked(vectorIndex.indexMemoryDeferred).mockImplementation((params) => insertIndexedRow(params, 'pending'));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294265:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:228:  vi.mocked(vectorIndex.deleteMemory).mockImplementation((id: number) => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294266:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:395:    const deleteMemoryCalls = vi.mocked(vectorIndex.deleteMemory).mock.calls.map(([memoryId]) => memoryId);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294267:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:442:    const deleteMemoryCalls = vi.mocked(vectorIndex.deleteMemory).mock.calls.map(([memoryId]) => memoryId);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294268:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:451:    const realDelete = vi.mocked(vectorIndex.deleteMemory).getMockImplementation();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294269:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:452:    vi.mocked(vectorIndex.deleteMemory).mockImplementation((id: number) => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294270:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:497:    expect(vi.mocked(vectorIndex.indexMemoryDeferred).mock.calls.length).toBeGreaterThanOrEqual(1);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294271:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:498:    expect(vi.mocked(vectorIndex.indexMemory).mock.calls.length).toBeGreaterThanOrEqual(1);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294272:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/chunking-orchestrator-swap.vitest.ts:557:  it('does not mutate parent BM25 document when all chunk inserts fail for an existing parent', async () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294273:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:31:    const vectorIndex = {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294274:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:35:      vectorSearch: vi.fn(),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294276:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:45:      vectorIndex,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294278:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:56:    expect(vectorIndex.closeDb).toHaveBeenCalled();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294279:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:57:    expect(vectorIndex.initializeDb).toHaveBeenCalled();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294280:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:58:    expect(hybridSearch.init).toHaveBeenCalledWith(fakeDb, vectorIndex.vectorSearch, fakeGraphFn);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294281:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:72:      const vectorIndex = {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294282:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:76:        vectorSearch: vi.fn(),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294284:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:85:        vectorIndex,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294286:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:99:      expect(vectorIndex.initializeDb).toHaveBeenCalledTimes(2);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294287:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:112:    const vectorIndex = {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294288:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:116:      vectorSearch: vi.fn(),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294290:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:125:      vectorIndex,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294292:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:138:  it('rebinds all registered database consumers when the vector index swaps connections directly', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294293:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:143:    const vectorIndex = {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294294:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:147:      vectorSearch: vi.fn(),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294296:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:164:      vectorIndex,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294298:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:174:    expect(vectorIndex.onDatabaseConnectionChange).toHaveBeenCalledTimes(1);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294299:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:181:    expect(hybridSearch.init).toHaveBeenCalledWith(reboundDb, vectorIndex.vectorSearch, null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294300:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:187:  it('logs when a direct vector-index rebind listener returns false', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294301:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:193:    const vectorIndex = {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294302:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:197:      vectorSearch: vi.fn(),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294303:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state-graph-reinit.vitest.ts:207:      vectorIndex,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294305:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:24:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294306:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:26:type VectorDb = NonNullable<ReturnType<typeof vectorIndex.getDb>>;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294307:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:49:/** Create a simple embedding vector of given dimension */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294308:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:218:      const getDbSpy = vi.spyOn(vectorIndex, 'getDb');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294309:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:243:      const getDbSpy = vi.spyOn(vectorIndex, 'getDb').mockReturnValue(asVectorDb(persistedDb.db));
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294310:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:656:    it('CS1: Identical vectors have similarity 1.0', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294311:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:662:    it('CS2: Orthogonal vectors have similarity 0.0', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294312:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:668:    it('CS3: Opposite vectors have similarity -1.0', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294313:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:674:    it('CS4: Different length vectors return 0', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294314:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/save-quality-gate.vitest.ts:680:    it('CS5: Zero vectors return 0', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294321:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/k-value-judged-sweep.vitest.ts:236:    // item-0 is rank 1 in vector results → NDCG should be perfect
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294322:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/k-value-judged-sweep.vitest.ts:254:        { source: SOURCE_TYPES.BM25,   results: results2 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294329:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:16:  source: 'vector';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294330:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:52:    { id: 1, similarity: 0.91, score: 0.91, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294331:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:53:    { id: 2, similarity: 0.88, score: 0.88, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294332:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts:54:    { id: 3, similarity: 0.85, score: 0.85, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294334:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294335:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294336:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:16:vi.mock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294337:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:38:import * as vectorIndex from '../lib/search/vector-index';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294338:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:86:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294339:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:123:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294340:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:199:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294341:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:243:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294342:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:296:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294343:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:321:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294344:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:387:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294345:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:439:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294346:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:481:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294347:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:504:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294348:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:554:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294349:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:572:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294350:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:589:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294351:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:612:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294352:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/dual-scope-hooks.vitest.ts:641:    vi.mocked(vectorIndex.getDb).mockReturnValue(null);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294353:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/temporal-contiguity.vitest.ts:68:      const boosted = mod.vectorSearchWithContiguity(results_arr, 3600); // 1-hour window
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294354:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/temporal-contiguity.vitest.ts:83:      const boosted = mod.vectorSearchWithContiguity(results_arr, 1800);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294355:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/temporal-contiguity.vitest.ts:99:      const boosted = mod.vectorSearchWithContiguity(results_arr, 3600); // 1 hour window
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294356:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/temporal-contiguity.vitest.ts:108:      const result = mod.vectorSearchWithContiguity([], 3600);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294357:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/temporal-contiguity.vitest.ts:114:      const result = mod.vectorSearchWithContiguity(null, 3600);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294358:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/temporal-contiguity.vitest.ts:182:    it('T502-09: vector contiguity clamps non-positive windows to minimum bound', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294359:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/temporal-contiguity.vitest.ts:189:      const boosted = mod.vectorSearchWithContiguity(results_arr, 0);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294362:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:11:  it('logs when a direct vector-index rebind listener returns false', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294363:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:17:    const vectorIndex = {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294364:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:21:      vectorSearch: vi.fn(),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294365:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:31:      vectorIndex,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294367:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:49:      vectorIndex: {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294368:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:75:      vectorIndex: {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294369:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/db-state.vitest.ts:99:      vectorIndex: {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294370:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/schema-migration.vitest.ts:6:import * as vectorIndex from '../lib/search/vector-index.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294372:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294373:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:31:import * as vectorIndex from '../lib/search/vector-index.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294375:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:38:const VECTOR_INDEX_QUERIES_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'lib', 'search', 'vector-index-queries.ts'), 'utf-8');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294377:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:40:const VECTOR_INDEX_SCHEMA_SOURCE = fs.readFileSync(path.join(SERVER_ROOT, 'lib', 'search', 'vector-index-schema.ts'), 'utf-8');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294378:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:175:      expect(typeof vectorIndex.multiConceptSearch).toBe('function');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294385:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:229:    it('T636: Hybrid combines vector + FTS', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294389:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:240:        { source: 'vector', results: [{ id: 1 }, { id: 2 }] },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294390:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:245:      expect(item!.sources).toContain('vector');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294392:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts:254:    it('T640: searchWithFallback falls back to BM25 after empty FTS results', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294396:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store.vitest.ts:12:} from '../lib/search/vector-index-store';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294397:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store.vitest.ts:59:describe('vector-index-store constitutional cache isolation', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294398:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/scoring/interference-scoring.ts:80: * This is a lightweight heuristic used when vector cosine similarity
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294399:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/feedback-denylist.vitest.ts:49:  const technicalTerms = ['vector', 'pipeline', 'database', 'embedding', 'reranker', 'checkpoint', 'ablation'];
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294401:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/quality-loop.vitest.ts:55:- Added BM25 baseline with configurable k1/b parameters
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294407:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:251:        makeRankedList('vector', [1, 2, 3]),
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294408:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294413:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:496:        sources: ['vector'],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294417:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:595:      const vectorResults: RrfItem[] = [
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294418:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:606:        { source: 'vector', results: vectorResults },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294420:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:659:      // Simulate: top-k only has vector results, but graph also returned results
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294421:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:661:        { id: 1, score: 0.9, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294422:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:662:        { id: 2, score: 0.8, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294423:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:663:        { id: 3, score: 0.7, source: 'vector' },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294424:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:667:        ['vector', [{ id: 1, score: 0.9 }, { id: 2, score: 0.8 }]],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294426:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:712:        { id: 1, rrfScore: 0.13, sources: ['vector', 'fts'], sourceScores: {}, convergenceBonus: 0.1 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294427:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/cross-feature-integration-eval.vitest.ts:713:        { id: 2, rrfScore: 0.08, sources: ['vector'], sourceScores: {}, convergenceBonus: 0 },
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294428:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:48:  // Normalize to unit vector for meaningful cosine similarity
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294429:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:290:      'The system uses vector embeddings for semantic search.',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294430:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:313:      'Cosine similarity measures vector closeness.',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294431:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:327:      'Beta sentence about embedding generation and vector storage.',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294432:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294433:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294434:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:456:    const queryEmb = await mockEmbeddingFn('search pipeline vector similarity retrieval');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294435:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:586:  it('returns 1.0 for identical vectors', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294436:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:591:  it('returns 0 for orthogonal vectors', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294437:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:597:  it('returns -1.0 for opposite vectors', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294438:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-summaries.vitest.ts:603:  it('returns 0 for zero-length vectors', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294440:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294446:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-schema-migration-refinements.vitest.ts:10:} from '../lib/search/vector-index-schema';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294447:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-schema-migration-refinements.vitest.ts:22:describe('vector-index schema migration refinements', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294448:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/tests/memory-context-session-state.vitest.ts:122:    vi.doMock('../lib/search/vector-index', () => ({
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294455:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:9:import * as vectorIndex from '../search/vector-index.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294456:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:292:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294457:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:442:  vectorIndex.initializeDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294458:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:443:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294459:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:491:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294460:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:507:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294461:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:561:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294462:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:567:    const memory = vectorIndex.getMemory(id);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294463:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:683:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294464:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:687:  const memory = vectorIndex.getMemory(id);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294465:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:719:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294466:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:725:  const memory = vectorIndex.getMemory(id);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294467:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:745:  const db = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294468:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:748:  const memory = vectorIndex.getMemory(id);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294469:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/providers/retry-manager.ts:945:  const memory = vectorIndex.getMemory(id) as RetryMemoryRow | undefined;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294470:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/utils/cleanup-helpers.ts:1:import { get_error_message } from '../search/vector-index-types.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294471:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/ops-hardening.ts:93:        'orphan_vectors',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294472:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/code-graph/query-intent-classifier.ts:6:// (CocoIndex) vs hybrid (both).
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294479:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/attention-decay.ts:16:// Search-time ranking      → FSRS-preferred SQL (vector-index-impl.js)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294480:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/temporal-contiguity.ts:51: * Apply temporal-contiguity boost to vector search results.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294481:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/temporal-contiguity.ts:63:export function vectorSearchWithContiguity(
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294482:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/archival-manager.ts:498:    console.warn(`[archival-manager] BM25 archive sync failed: ${msg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294484:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/archival-manager.ts:539:    console.warn(`[archival-manager] BM25 unarchive sync failed: ${msg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294485:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/archival-manager.ts:544: * Defer vector re-embedding to the next index scan rather than rebuilding immediately.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294486:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/archival-manager.ts:554:    `[archival-manager] Deferred vector re-embedding for memory ${memoryId} until next index scan`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294491:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/co-activation.ts:271:  vectorSearchFn: (embedding: Float32Array, options: Record<string, unknown>) => Array<{ id: number; similarity: number; [key: string]: unknown }>
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294492:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.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/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294493:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/co-activation.ts:295:    const similar = vectorSearchFn(embedding, {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294494:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/cognitive/co-activation.ts:367: * that pure vector similarity would miss.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294537:151:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294543:616:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294552:1077:22:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294555:1430:4951:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294560:1556:6006:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294562:1574:6093:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294564:1587:6154:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294565:1591:6174:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294572:2453:19159:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294575:2655:21326:.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/004-opencode-mnemosyne-main/research/research.md:294576:2833:21930:.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-graph-context-systems/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/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294578:3641:209104:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:4938:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294582:3683:209151:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:6963:51302:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294586:3742:209249:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7173:55965:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294587:3761:209274:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7229:58167:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/phase-research-prompt.md:9:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294589:3773:209287:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7265:58212:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-004.md:78:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294590:3786:209300:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7349:58501:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-005.md:64:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294593:3801:209315:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7386:58569:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:9:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294594:3814:209328:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7430:58649:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:4938:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294595:3827:209341:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7470:58707:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:5993:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294596:3833:209347:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7481:58727:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:6080:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294598:3837:209351:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7487:58738:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-006.md:75:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294602:3859:209373:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7539:58829:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-008.md:60:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294604:3887:209403:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7602:58959:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-007.md:65:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294607:3917:209433:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7725:59275:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:49:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294608:3919:209435:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7729:59280:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:69:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294609:3932:209448:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7762:59376:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-003.md:64:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294615:3965:209483:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7885:60543:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294616:3971:209489:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7894:60620:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294617:3976:209494:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7902:60676:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294618:3978:209496:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7905:60694:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294619:4019:209547:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7990:66987:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294623:4062:209651:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8189:80046:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294627:4109:209718:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8353:86915:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294631:4145:209768:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8555:93666:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294633:4184:209819:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8681:98710:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294635:4195:209834:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8719:99503:    73	Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294636:4204:209845:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8750:99703:     9	Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294637:4238:209889:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8832:103195:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294638:4266:209923:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:8972:114892:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294642:4308:209979:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:9069:121898:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294646:4343:210029:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:9216:125594:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294647:4372:210066:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:9320:130836:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294651:4391:210093:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:9385:131285:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294653:4414:210125:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:9443:132029:    69	Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294661:4492:210303:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294662:4525:210498:.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/004-opencode-mnemosyne-main/research/research.md:294698:6168:- Re-platforming Public’s retrieval or mutation core around Mnemosyne should remain rejected; the transferable value is wrapper ergonomics and compaction behavior, not replacing Public’s hybrid pipeline or CocoIndex separation.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294717:6269:- Re-platforming Public’s retrieval or mutation core around Mnemosyne should remain rejected; the transferable value is wrapper ergonomics and compaction behavior, not replacing Public’s hybrid pipeline or CocoIndex separation.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294760:142:- Re-platforming Public’s retrieval or mutation core around Mnemosyne should remain rejected; the transferable value is wrapper ergonomics and compaction behavior, not replacing Public’s hybrid pipeline or CocoIndex separation.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294762:161:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294857:141:- Re-platforming Public’s retrieval or mutation core around Mnemosyne should remain rejected; the transferable value is wrapper ergonomics and compaction behavior, not replacing Public’s hybrid pipeline or CocoIndex separation.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294865:181:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294954:122:- Re-platforming Public’s retrieval or mutation core around Mnemosyne should remain rejected; the transferable value is wrapper ergonomics and compaction behavior, not replacing Public’s hybrid pipeline or CocoIndex separation.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294974:203:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294983:3350:.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/004-opencode-mnemosyne-main/research/research.md:294987:4407:.opencode/skills/system-spec-kit/mcp_server/tests/interfaces.vitest.ts:347:    it('MockVectorStore rejects mismatched embedding dimensions', async () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294989:5566:.opencode/skills/system-spec-kit/mcp_server/tests/local-reranker.vitest.ts:14:  it('rejects embedding-like arrays and payloads', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294990:5788:.opencode/skills/system-spec-kit/mcp_server/tests/orchestrator-error-cascade.vitest.ts:174:    await expect(executePipeline(config)).rejects.toThrow('embedding service unavailable');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294991:6388:.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1294:    it('indexMemory rejects wrong embedding dimension', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:294992:6391:.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts:1306:    it('indexMemory rejects null embedding', () => {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295012:11525:### Finding 7: CocoIndex should stay separate from memory retrieval because its indexing and refresh costs are materially different
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295032:11624:### Finding 7: CocoIndex should stay separate from memory retrieval because its indexing and refresh costs are materially different
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295068:93:- Re-platforming Public’s retrieval or mutation core around Mnemosyne should remain rejected; the transferable value is wrapper ergonomics and compaction behavior, not replacing Public’s hybrid pipeline or CocoIndex separation.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295099:215:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295109:4591:### Finding 3: Mnemosyne should remain memory-only and must not be fused with CocoIndex or code-graph routing
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295117:4636:- Questions answered: `[Mnemosyne’s best transfer is prompt-level memory discipline and a thin ergonomic facade; its project/global scope model conflicts with governed Public scope; its memory surface should stay separate from CocoIndex and code-graph routing; any adoption should delegate into Public’s existing recovery/save authority rather than create a second backend]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295125:4689:### Finding 3: Mnemosyne should remain memory-only and must not be fused with CocoIndex or code-graph routing
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295133:4734:- Questions answered: `[Mnemosyne’s best transfer is prompt-level memory discipline and a thin ergonomic facade; its project/global scope model conflicts with governed Public scope; its memory surface should stay separate from CocoIndex and code-graph routing; any adoption should delegate into Public’s existing recovery/save authority rather than create a second backend]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295157:69:- Re-platforming Public’s retrieval or mutation core around Mnemosyne should remain rejected; the transferable value is wrapper ergonomics and compaction behavior, not replacing Public’s hybrid pipeline or CocoIndex separation.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295196:232:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295208:3424:.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/004-opencode-mnemosyne-main/research/research.md:295209:4208:    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/004-opencode-mnemosyne-main/research/research.md:295306:237:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295315:7684:    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/004-opencode-mnemosyne-main/research/research.md:295316:8312:.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/004-opencode-mnemosyne-main/research/research.md:295317:8564:.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/004-opencode-mnemosyne-main/research/research.md:295318:8567:.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/004-opencode-mnemosyne-main/research/research.md:295319:8734:.opencode/skills/system-spec-kit/mcp_server/dist/tool-schemas.js:18:    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/004-opencode-mnemosyne-main/research/research.md:295349:12504:- Questions answered: `[retrieval core stays Public-owned, compaction should extend existing transport, project/global must be facade-only, core must map to constitutional memory, session_bootstrap/causal/CocoIndex remain first-class]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295365:12626:- Questions answered: `[retrieval core stays Public-owned, compaction should extend existing transport, project/global must be facade-only, core must map to constitutional memory, session_bootstrap/causal/CocoIndex remain first-class]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295429:253:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295460:1205:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-010.md:46:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295584:1606:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-035.md:4636:- Questions answered: `[Mnemosyne’s best transfer is prompt-level memory discipline and a thin ergonomic facade; its project/global scope model conflicts with governed Public scope; its memory surface should stay separate from CocoIndex and code-graph routing; any adoption should delegate into Public’s existing recovery/save authority rather than create a second backend]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295587:1616:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-035.md:4734:- Questions answered: `[Mnemosyne’s best transfer is prompt-level memory discipline and a thin ergonomic facade; its project/global scope model conflicts with governed Public scope; its memory surface should stay separate from CocoIndex and code-graph routing; any adoption should delegate into Public’s existing recovery/save authority rather than create a second backend]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295653:1820:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:5993:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295655:1827:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:6080:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295660:1845:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:1556:6006:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295661:1847:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:1574:6093:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295662:1849:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:1587:6154:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295675:1873:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:3827:209341:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7470:58707:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:5993:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295676:1875:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:3833:209347:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7481:58727:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:6080:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295684:1889:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:3917:209433:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7725:59275:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:49:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295690:1897:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:3965:209483:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7885:60543:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295691:1898:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:3971:209489:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7894:60620:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295692:1899:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-031.md:3976:209494:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7902:60676:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295759:2073:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:49:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295808:2241:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-030.md:6566:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-010.md:46:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295818:2261:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-030.md:7389:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7470:58707:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:5993:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295819:2263:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-030.md:7395:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7481:58727:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:6080:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295827:2277:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-030.md:7481:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7725:59275:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:49:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295833:2285:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-030.md:7531:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7885:60543:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295834:2286:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-030.md:7537:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7894:60620:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295835:2287:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-030.md:7542:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7902:60676:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295873:2389:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-009.md:2808:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:5993:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295874:2392:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-009.md:2828:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:6080:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295882:2418:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-009.md:3376:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:49:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295889:2447:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-009.md:4644:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295891:2454:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-009.md:4721:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295982:2884:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:5735:- Questions answered: **yes** — the strongest paradigm shifts are **multi-plane memory architecture, autonomy-stage governance, proposal-first mutation, decay-as-workflow, and readiness-aware mission state**. The delta is now more about **memory operations architecture** than about BM25 or FSRS formulas.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295983:2889:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:5984:6006:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295984:2891:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:5997:6093:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:295985:2893:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:6008:6154:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296010:2944:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7470:58707:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:5993:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296011:2946:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7481:58727:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:6080:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296019:2963:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7725:59275:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:49:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296025:2975:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7885:60543:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296026:2977:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7894:60620:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296027:2979:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7902:60676:- Questions answered: Mnemosyne’s lifecycle is storage-first and instruction-driven; Public’s lifecycle is session-first and contract-driven. The strongest reusable ideas are lightweight project/global ergonomics and optional compaction reminders, but Mnemosyne’s stateless tool boundary, basename-derived identity, and string-only session save model should not replace `memory_context`, `generate-context.js`, or `session_bootstrap`. The exact strict validation command passed with `RESULT: PASSED` and `Summary: Errors: 0  Warnings: 0`, alongside the expected read-only warning `cannot create temp file for here document: Operation not permitted`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296081:3122:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-037.md:12504:- Questions answered: `[retrieval core stays Public-owned, compaction should extend existing transport, project/global must be facade-only, core must map to constitutional memory, session_bootstrap/causal/CocoIndex remain first-class]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296084:3132:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-037.md:12626:- Questions answered: `[retrieval core stays Public-owned, compaction should extend existing transport, project/global must be facade-only, core must map to constitutional memory, session_bootstrap/causal/CocoIndex remain first-class]`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296089:5462:.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/004-opencode-mnemosyne-main/research/research.md:296094:5910:1556:6006:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296095:5912:1574:6093:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296096:5914:1587:6154:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296109:5938:3827:209341:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7470:58707:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:5993:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296110:5940:3833:209347:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7481:58727:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-001.md:6080:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296118:5954:3917:209433:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7725:59275:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-002.md:49:- Questions answered: the wrapper is thin; hybrid ranking is README-level not wrapper-owned; Public already has deeper hybrid retrieval; project/global split is useful but collision-prone; compaction tool reminders are the best adopt-now idea; CocoIndex should stay separate from memory retrieval
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296122:5960:3950:209468:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-021.md:7822:59613:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/iterations/iteration-006.md:5868:- Questions answered: Mnemosyne’s wrapper exposes no dedup, no upsert, no revision lineage, no soft-delete lifecycle, and no retention/GC contract; contradiction hygiene is primarily agent guidance plus hard delete; basename-derived project scoping is materially less stable than Public’stcher-delete-rename-cleanup.md:21:- Pass/fail: PASS if stale paths are removed, renamed paths are reindexed, and no orphaned entries remain after delete, rename, burst-rename, or concurrent-rename flows\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/16--tooling-and-scripts/207-watcher-delete-rename-cleanup.md:29:| 207 | Watcher delete/rename cleanup | Confirm delete and rename cleanup remove stale index state | `Validate watcher delete/rename cleanup. Capture the evidence needed to prove unlink events call removeFn for deleted markdown files; rename is handled as old-path cleanup plus new-path indexing; the default 2-second debounce window collapses rapid rename/change bursts into a single stable reindex; and burst or concurrent renames leave only the final live paths indexed. Return a concise user-facing pass/fail verdict with the main reason.` | 1) run the file-watcher Vitest suite and capture the delete/unlink scenario where removeFn is called for a deleted markdown file 2) capture the rename lifecycle scenario showing unlink on the old path and add on the new path 3) capture the default-window debounce scenario proving rapid changes within the 2-second window coalesce to one reindex 4) capture the burst-rename scenario showing only the final path remains indexed 5) capture the concurrent-rename scenario showing every stale path is removed and every renamed path is indexed | unlink events call removeFn for deleted markdown files; rename removes the old path and indexes the new path; the default 2-second debounce window collapses rapid rename/change bursts to one stable reindex; burst renames keep only the final path indexed; concurrent renames remove all stale paths and keep all renamed paths indexed | Vitest output for delete/unlink, rename lifecycle, default debounce, burst rename, and concurrent rename cases + any logged indexed-path snapshots used to prove stale entries were removed | PASS if stale paths are removed, renamed paths are reindexed, and no orphaned entries remain after delete, rename, burst-rename, or concurrent-rename flows | Inspect `mcp_server/lib/ops/file-watcher.ts` debounce scheduling, unlink handling, and `removeFn` wiring if stale entries persist or rename paths duplicate |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/core/file-writer.ts:24:    .replace(/^(created_at|created_at_epoch|last_accessed_epoch|expires_at_epoch):.*$/gm, '$1: <normalized>')\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/146-dynamic-server-instructions-p1-6.md:3:description: \\\"This scenario validates Dynamic server instructions (P1-6) for `146`. It focuses on Verify `setInstructions()` is called at MCP startup with memory count, spec folder count, channel list, and stale warning.\\\"\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/146-dynamic-server-instructions-p1-6.md:10:This scenario validates Dynamic server instructions (P1-6) for `146`. It focuses on Verify `setInstructions()` is called at MCP startup with memory count, spec folder count, channel list, and stale warning.\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/146-dynamic-server-instructions-p1-6.md:18:- Objective: Verify `setInstructions()` is called at MCP startup with memory count, spec folder count, channel list, and stale warning\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/146-dynamic-server-instructions-p1-6.md:19:- Prompt: `Validate dynamic server instructions at MCP initialization. Capture the evidence needed to prove Startup instructions include memory system overview with counts and channels; stale warning appears only above threshold; disabled flag yields empty instructions. Return a concise user-facing pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/146-dynamic-server-instructions-p1-6.md:20:- Expected signals: Startup instructions include memory system overview with counts and channels; stale warning appears only above threshold; disabled flag yields empty instructions\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/146-dynamic-server-instructions-p1-6.md:29:| 146 | Dynamic server instructions (P1-6) | Verify `setInstructions()` is called at MCP startup with memory count, spec folder count, channel list, and stale warning | `Validate dynamic server instructions at MCP initialization. Capture the evidence needed to prove Startup instructions include memory system overview with counts and channels; stale warning appears only above threshold; disabled flag yields empty instructions. Return a concise user-facing pass/fail verdict with the main reason.` | 1) Start the MCP server and capture startup logs 2) Verify `setInstructions()` was called with a non-empty instructions string 3) Verify instructions include: memory count, spec folder count, available channels, and active feature flags 4) If 11+ stale memories exist, verify a stale warning is included 5) Restart with `SPECKIT_DYNAMIC_INIT=false` and verify `setInstructions()` receives an empty string | Startup instructions include memory system overview with counts and channels; stale warning appears only above threshold; disabled flag yields empty instructions | Server startup log + instructions content snapshot + flag toggle comparison | PASS if enabled mode emits overview with counts/channels and disabled mode yields empty string | Inspect `context-server.ts` `buildServerInstructions`, `startup-checks.ts`, and `SPECKIT_DYNAMIC_INIT` flag handling |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/16--tooling-and-scripts/183-runtime-lineage-naming-parity.md:22:- Prompt: `Audit runtime agent naming parity. Capture the evidence needed to prove base (.opencode/agents/) matches Claude and Gemini, Codex traces lineage to base after extension normalization, deep-research is the active name, and stale research naming is absent. Return a concise pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/16--tooling-and-scripts/183-runtime-lineage-naming-parity.md:32:- Pass: normalized basenames match and no stale naming.\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/test-scripts-modules.js:2062:      pass('T-032a: scripts retry-manager module removed', 'No stale scripts/lib retry-manager output');\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/204-embedding-retry-orchestrator.md:29:| 204 | Embedding retry orchestrator | Verify failed embeddings fall back to pending lexical-only storage and are later repaired by the background retry manager with retry/backoff tracking | \\\"Validate the embedding retry orchestrator. Capture the evidence needed to prove a save or index operation can persist a memory with `embedding_status='pending'` when the provider is unavailable; the retry manager later picks up pending items in batch; cache dedup avoids redundant embedding calls where possible; retry counts/backoff state advance on repeated failures; and a successful retry refreshes the stored vector/index state. Return a concise user-facing pass/fail verdict with the main reason.\\\" | 1) Simulate embedding-provider unavailability during `memory_save` or `memory_index_scan` 2) Confirm the memory is still saved and marked pending without vectors, with lexical-only fallback intact 3) Restore provider availability and run or wait for the retry manager batch job 4) Confirm pending items are retried, retry counters/backoff metadata update appropriately, and cache reuse is visible when content was embedded before 5) Verify successful retry clears the pending state and refreshes vector/index rows for the affected memory | Provider outage yields saved memory with pending embedding status and lexical-only fallback; retry manager scans and processes pending items; embedding cache participates in deduplication; retry count/progressive backoff state changes across failures; successful retry updates memory index and vector storage | Save/index transcript during outage + pending status evidence + retry-manager run output + cache/retry stats + final vector/index state after recovery | PASS if pending memories remain searchable lexically during outage and are later upgraded with vectors by retry orchestration; FAIL if failed embeddings are dropped, pending items are never retried, or success does not refresh index/vector state | Inspect retry-manager batch selection and backoff logic; verify embedding cache reuse; check pending-status persistence during fallback; confirm retry success path clears stale vector rows and writes refreshed embeddings |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/core/workflow.ts:399:    // Best-effort stale lock cleanup.\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/progressive-validation.vitest.js:21://   T-PB2-12  --level 2 runs detect + auto-fix only\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/workflow-e2e.vitest.ts:421:    const dataFile = writeInputFile(harness, 'stale-lock.json', createExplicitJsonInput());\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/workflow-e2e.vitest.ts:425:    const staleAt = new Date(Date.now() - 10_000);\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/workflow-e2e.vitest.ts:426:    fs.utimesSync(WORKFLOW_LOCK_DIR, staleAt, staleAt);\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/112-cross-process-db-hot-rebinding.md:19:- Prompt: `Validate cross-process DB hot rebinding via marker file. Capture the evidence needed to prove Server detects DB_UPDATED_FILE marker; DB reinitializes without restart; stats reflect post-mutation state (no stale data); health reports healthy after rebind. Return a concise user-facing pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/112-cross-process-db-hot-rebinding.md:20:- Expected signals: Server detects DB_UPDATED_FILE marker; DB reinitializes without restart; stats reflect post-mutation state (no stale data); health reports healthy after rebind\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/112-cross-process-db-hot-rebinding.md:21:- Pass/fail: PASS if server detects marker file, reinitializes DB, returns current (non-stale) data, and health is healthy\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/112-cross-process-db-hot-rebinding.md:29:| 112 | Cross-process DB hot rebinding | Confirm marker-file triggers DB reinitialization | `Validate cross-process DB hot rebinding via marker file. Capture the evidence needed to prove Server detects DB_UPDATED_FILE marker; DB reinitializes without restart; stats reflect post-mutation state (no stale data); health reports healthy after rebind. Return a concise user-facing pass/fail verdict with the main reason.` | 1) start MCP server 2) create a test memory via MCP: `memory_save(filePath)` and note its title 3) from a separate terminal, run `node cli.js bulk-delete --tier scratch --folder specs/test-sandbox` (non-dry-run — this mutates the DB and writes the `DB_UPDATED_FILE` marker) 4) immediately call `memory_stats()` via MCP → verify server detects marker and reinitializes DB 5) verify no stale data from pre-rebind state 6) run `memory_health()` → verify healthy status post-rebind | Server detects DB_UPDATED_FILE marker; DB reinitializes without restart; stats reflect post-mutation state (no stale data); health reports healthy after rebind | memory_stats output post-rebind + memory_health output + marker file detection evidence | PASS if server detects marker file, reinitializes DB, returns current (non-stale) data, and health is healthy | Inspect DB_UPDATED_FILE marker path and detection logic; verify DB reinitialization clears caches; check for stale connection handles |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/coverage-graph-signals.vitest.ts:131:      graph.nodes.set('stale', { id: 'stale' });\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/coverage-graph-signals.vitest.ts:132:      const momentum = signalsModule.computeMomentum(graph, 'stale', 300000);\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/evals/check-source-dist-alignment.ts:11://   2026-03-07. No matching source remains, so the stale dist\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/evals/check-source-dist-alignment.ts:16://   mcp_server/lib/eval/memory-state-baseline.ts, so the stale\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/evals/check-source-dist-alignment.ts:181:    console.error('\\\\nRemove stale dist outputs, restore missing source files, or add a time-bounded allowlist entry.');\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/16--tooling-and-scripts/151-module-map-accuracy.md:37:| 151 | MODULE_MAP.md accuracy | Verify 5 module entries match actual code | `Validate MODULE_MAP.md accuracy by spot-checking 5 modules (config, cognitive, search, storage, scoring). For each: verify listed key files exist, verify primary consumers are accurate via grep. Return a pass/fail verdict per module.` | 1) `cd .opencode/skills/system-spec-kit` 2) Read MODULE_MAP.md entries for config, cognitive, search, storage, scoring 3) For each module: `ls mcp_server/lib/{module}/` to verify key files exist 4) For each module: `grep -r \\\"from.*/{module}/\\\" mcp_server/ --include=\\\"*.ts\\\" -l` to verify consumers 5) Compare against MODULE_MAP.md listings | All 5 modules have accurate file lists and consumer mappings | ls output + grep output per module vs MODULE_MAP.md entries | PASS if all 5 sampled modules are accurate | Identify stale entry -> update MODULE_MAP.md -> re-verify |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/memory-quality-phase6-template.test.ts:403:    expect(rewrite.content).not.toContain('  - \\\"stale metadata trigger\\\"');\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/218-mcp-server-public-api-barrel.md:29:| 218 | MCP Server Public API Barrel | Verify the top-level barrel re-exports the approved runtime, helper, and metadata surfaces from one stable import boundary | `Validate the MCP server public API barrel. Capture the evidence needed to prove external consumers can import approved evaluation, indexing, search, provider, storage, helper, and rollout-metadata surfaces from \\\\`mcp_server/api\\\\` without deep-linking into internal \\\\`lib/\\\\`, \\\\`core/\\\\`, or \\\\`handlers/\\\\` modules, and that the README reinforces this contract. Return a concise user-facing pass/fail verdict with the main reason.` | 1) Inspect `mcp_server/api/index.ts` and capture the top-level export groups and promoted helper surfaces 2) Cross-check those exports against `api/eval.ts`, `api/indexing.ts`, `api/search.ts`, `api/providers.ts`, and `api/storage.ts` plus the curated internal helper modules named in the catalog 3) Inspect `mcp_server/api/README.md` and confirm consumer guidance points to `api/` as the supported boundary 4) Run a barrel import smoke test or equivalent script check that accesses representative symbols from each export family through `mcp_server/api` only | `mcp_server/api/index.ts` re-exports the documented evaluation, indexing, search, provider, storage, helper, and metadata symbols; `mcp_server/api/README.md` names `api/` as the approved public surface; consumers can rely on one stable top-level barrel | Barrel export capture + README policy snippet + cross-check notes against sub-barrels and curated helper sources + import smoke-test transcript or equivalent proof | PASS if the barrel centralizes the approved public import contract and the docs steer consumers to `api/`; FAIL if required exports are missing, helper surfaces require internal imports, or the docs contradict the barrel policy | Inspect `mcp_server/api/index.ts` for stale or missing re-exports -> verify renamed helper symbols still match the barrel contract -> check `mcp_server/api/README.md` for outdated consumer guidance -> confirm callers are not forced back to internal paths for metadata or rollout helpers |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/session-cached-consumer.vitest.ts.test.ts:209:  it('matches the frozen corpus outcomes for stale, scope mismatch, fidelity failure, and valid reuse', () => {\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/session-cached-consumer.vitest.ts.test.ts:212:        name: 'stale',\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/session-cached-consumer.vitest.ts.test.ts:217:        expected: { status: 'rejected', category: 'freshness', reason: 'stale_summary' },\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/scripts/tests/session-cached-consumer.vitest.ts.test.ts:354:        name: 'stale',\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/04--maintenance/014-workspace-scanning-and-indexing-memory-index-scan.md:19:- Prompt: `Run the incremental scan flow and the targeted atomic lease checks for memory_index_scan. Capture the evidence needed to prove scan summary and updated index state, that spec documents remain indexed in warn-only quality mode, and that scan leases reserve scan_started_at atomically, reject overlapping fresh scans, expire stale crashed-scan leases, and only move to last_index_scan on completion. Return a concise user-facing pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/04--maintenance/014-workspace-scanning-and-indexing-memory-index-scan.md:20:- Expected signals: Scan summary, updated index state, spec-doc warn-only indexing behavior, atomic lease reservation, rejection wait time, stale-lease expiry, and completion handoff to `last_index_scan`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/04--maintenance/014-workspace-scanning-and-indexing-memory-index-scan.md:32:| EX-014 | Workspace scanning and indexing (memory_index_scan) | Stale crashed-scan leases expire and allow a fresh reservation | `Run the stale-lease expiry validation. Capture the evidence needed to prove an expired scan_started_at lease is cleared and replaced by a fresh reservation so crashed scans do not block future indexing forever. Return a concise user-facing pass/fail verdict with the main reason.` | `cd .opencode/skills/system-spec-kit/mcp_server` -> `npm test -- --run tests/db-state.vitest.ts -t \\\"expires stale scan lease and allows a fresh reservation\\\"` | Expired `scan_started_at` is removed and the new reservation succeeds | Targeted test transcript showing stale-lease expiry and fresh reservation | PASS if the targeted test passes and the refreshed lease uses the current reservation timestamp | Inspect `core/db-state.ts` `clearStaleScanLease()` and `SPECKIT_INDEX_SCAN_LEASE_EXPIRY_MS` handling if expired leases keep blocking scans |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/042-spec-folder-description-discovery-pi-b3.md:19:- Prompt: `Validate PI-B3 folder description discovery. Capture the evidence needed to prove description.json exists after create.sh; stale detection triggers on spec.md edit; per-folder files preferred over spec.md fallback; mixed-mode aggregation works; invalid JSON or schema-invalid description.json files are ignored, spec.md fallback is used, and existing files are repaired in place; missing description.json falls back cleanly without implicit backfill; out-of-base or prefix-bypass paths are rejected by realpath containment checks; YAML frontmatter is stripped before description extraction, including CRLF-heavy frontmatter cases; memory_context uses folder routing; regeneration leaves valid JSON on disk with no leftover temp files. Return a concise user-facing pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/042-spec-folder-description-discovery-pi-b3.md:20:- Expected signals: description.json exists after create.sh; stale detection triggers on spec.md edit; per-folder files preferred over spec.md fallback; mixed-mode aggregation works; invalid JSON or schema-invalid description.json files are ignored, spec.md fallback is used, and existing files are repaired in place; missing description.json falls back cleanly without implicit backfill; out-of-base or prefix-bypass paths are rejected by realpath containment checks; YAML frontmatter is stripped before description extraction, including CRLF-heavy frontmatter cases; memory_context uses folder routing; regeneration leaves valid JSON on disk with no leftover temp files\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/042-spec-folder-description-discovery-pi-b3.md:21:- Pass/fail: PASS: description.json created, stale detection works, per-folder preferred, mixed aggregation correct, no crash on corrupt description.json, invalid metadata repaired on regeneration, missing files fall back without implicit writes, traversal attempts rejected, frontmatter stripping works for CRLF-heavy files, folder routing active, and regenerated files are valid JSON with no leftover temp files; FAIL: Any of the scenario checks fails\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/042-spec-folder-description-discovery-pi-b3.md:29:| 042 | Spec folder description discovery (PI-B3) | Confirm per-folder + aggregated routing | `Validate PI-B3 folder description discovery. Capture the evidence needed to prove description.json exists after create.sh; stale detection triggers on spec.md edit; per-folder files preferred over spec.md fallback; mixed-mode aggregation works; invalid JSON or schema-invalid description.json files are ignored, spec.md fallback is used, and existing files are repaired in place; missing description.json falls back cleanly without implicit backfill; out-of-base or prefix-bypass paths are rejected by realpath containment checks; YAML frontmatter is stripped before description extraction, including CRLF-heavy frontmatter cases; memory_context uses folder routing; regeneration leaves valid JSON on disk with no leftover temp files. Return a concise user-facing pass/fail verdict with the main reason.` | 1) Create spec folder via create.sh → verify description.json exists 2) Edit spec.md → verify isPerFolderDescriptionStale detects change 3) Run generateFolderDescriptions → verify per-folder files preferred over spec.md 4) Mixed mode: some folders with/without description.json → verify aggregation 5) Corrupt description.json with invalid JSON and schema-invalid field types → run generateFolderDescriptions() and verify spec.md fallback plus repaired description.json 6) Verify missing description.json falls back to spec.md without forcing a write 7) Attempt generation against an out-of-base or prefix-bypass path → verify rejection and no file written 8) Use spec.md with large YAML frontmatter and CRLF-heavy line endings → verify extracted description comes from post-frontmatter content 9) Run memory_context query → verify short-circuit folder routing | description.json exists after create.sh; stale detection triggers on spec.md edit; per-folder files preferred over spec.md fallback; mixed-mode aggregation works; invalid JSON or schema-invalid description.json files are ignored, spec.md fallback is used, and existing files are repaired in place; missing description.json falls back cleanly without implicit backfill; out-of-base or prefix-bypass paths are rejected by realpath containment checks; YAML frontmatter is stripped before description extraction, including CRLF-heavy frontmatter cases; memory_context uses folder routing; regeneration leaves valid JSON on disk with no leftover temp files | description.json content + stale detection output + folder routing trace in memory_context + recovery evidence for corrupt/schema-invalid description.json files + missing-file fallback evidence + rejection evidence for traversal attempts + proof of valid regenerated JSON with no leftover temp files | PASS: description.json created, stale detection works, per-folder preferred, mixed aggregation correct, no crash on corrupt description.json, invalid metadata repaired on regeneration, missing files fall back without implicit writes, traversal attempts rejected, frontmatter stripping works for CRLF-heavy files, folder routing active, and regenerated files are valid JSON with no leftover temp files; FAIL: Any of the scenario checks fails | Verify create.sh generates description.json → Check stale detection mtime comparison → Inspect generateFolderDescriptions preference logic and repair path → Confirm missing-file fallback does not backfill unexpectedly → Verify realpath containment rejects traversal/prefix-bypass paths → Confirm frontmatter stripping happens before description extraction → Verify memory_context folder routing |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/044-reconsolidation-on-save-tm-06.md:10:This scenario validates Reconsolidation-on-save (TM-06) for `044`. It focuses on confirming merge/deprecate thresholds plus the stale-predecessor and BM25-repair safety paths.\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/044-reconsolidation-on-save-tm-06.md:18:- Objective: Confirm merge/deprecate thresholds plus stale-merge abort and BM25 repair-flag persistence\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/044-reconsolidation-on-save-tm-06.md:19:- Prompt: `Validate reconsolidation-on-save (TM-06). Capture the evidence needed to prove Similarity >=0.88 triggers merge; 0.75-0.88 triggers supersede/deprecate; below 0.75 saves independently; stale predecessor changes abort merge with predecessor_changed or predecessor_gone; and failed post-commit BM25 repair persists bm25_repair_needed=1 on the merged row. Return a concise user-facing pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/044-reconsolidation-on-save-tm-06.md:20:- Expected signals: Similarity >=0.88 triggers merge; 0.75-0.88 triggers supersede/deprecate; below 0.75 saves independently; stale predecessor changes abort merge instead of archiving/inserting; BM25 repair failure leaves merged lineage committed and sets `bm25_repair_needed=1`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/044-reconsolidation-on-save-tm-06.md:21:- Pass/fail: PASS: Threshold behavior is correct, stale predecessor writes return `predecessor_changed` or `predecessor_gone` without destructive merge side effects, and failed BM25 repair persists `bm25_repair_needed=1`; FAIL: Wrong threshold action, stale merge still commits, or BM25 repair debt is not recorded\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/044-reconsolidation-on-save-tm-06.md:30:| 044 | Reconsolidation-on-save (TM-06) | Abort stale merge when predecessor changes before commit | `Validate reconsolidation-on-save (TM-06) stale-predecessor protection. Reproduce a case where executeMerge() snapshots a predecessor, another writer updates that predecessor during embedding generation, and the merge path returns predecessor_changed or predecessor_gone instead of archiving/inserting a stale merged row. Capture the evidence needed to prove the original predecessor remains the only active row after the abort. Return a concise user-facing pass/fail verdict with the main reason.` | 1) Seed a merge-eligible predecessor with known `content_hash` and `updated_at` 2) start merge with async embedding generation 3) mutate, archive, or delete the predecessor before the transaction body resumes 4) verify complement-style abort with `predecessor_changed` or `predecessor_gone` 5) verify no merged row was inserted and predecessor lineage stayed intact 6) `npx vitest run .opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts -t \\\\\\\"Aborts merge when predecessor changes during embedding generation\\\\\\\"` | Merge returns `action: complement` with `status: predecessor_changed` or `status: predecessor_gone`; no stale merged row is inserted; predecessor row reflects only the concurrent writer change | Targeted vitest output plus `memory_index` row dump showing the predecessor remained active and no new merged row was created | PASS: Stale predecessor detection blocks the merge and preserves the current predecessor state; FAIL: Merge still archives/inserts despite predecessor mutation or deletion | Verify predecessor snapshot capture (`content_hash`, `updated_at`) → Check in-transaction reload → Inspect `hasPredecessorChanged()` branch → Confirm archive/delete handling |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/196-tool-level-ttl-cache.md:19:- Prompt: `Verify the tool-level TTL cache on a repeated expensive request. Run the same request twice within the active TTL window and confirm the second run is served from the per-tool cache using the same SHA-256 cache key. Then invalidate the relevant search path with a mutation or wait for TTL expiry and verify the next run recomputes instead of serving stale data. Capture hit, miss, eviction or invalidation evidence and return a concise user-facing pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/196-tool-level-ttl-cache.md:20:- Expected signals: first run records a cache miss for the tool/input combination; second identical run records a cache hit for the same SHA-256 key; cache stats reflect hits, misses, and invalidations; a relevant mutation or TTL expiry forces recomputation instead of returning stale results\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/196-tool-level-ttl-cache.md:21:- Pass/fail: PASS: identical repeat work hits the cache within TTL and recomputes after targeted invalidation or TTL expiry; FAIL: repeat work misses unexpectedly, stale data survives mutation/expiry, or cache accounting contradicts observed behavior\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/196-tool-level-ttl-cache.md:29:| 196 | Tool-level TTL cache | Confirm per-tool cache hits, TTL expiry, and mutation-driven invalidation | `Verify the tool-level TTL cache on a repeated expensive request. Run the same request twice within the active TTL window and confirm the second run is served from the per-tool cache using the same SHA-256 cache key. Then invalidate the relevant search path with a mutation or wait for TTL expiry and verify the next run recomputes instead of serving stale data. Capture hit, miss, eviction or invalidation evidence and return a concise user-facing pass/fail verdict with the main reason.` | 1) Confirm current cache settings, including active TTL window 2) Run a repeatable expensive request such as the same `memory_search` twice with identical inputs 3) Inspect cache stats or trace output to confirm miss then hit on the same tool/input key 4) Perform a relevant mutation such as `memory_save`, `memory_update`, or `memory_delete`, or wait past TTL expiry 5) Re-run the same request and confirm recomputation plus invalidation or expiry accounting | First run is a miss; second identical run is a hit; cache key is stable for identical tool+input; stats show hit/miss/invalidation activity; post-mutation or post-expiry run recomputes instead of returning stale data | Terminal transcript, cache stats or logs, repeated request output, and post-mutation or post-expiry rerun evidence | PASS: second identical run is a cache hit and the next run after invalidation or expiry recomputes cleanly; FAIL: repeated request misses inside TTL, stale results survive invalidation, or stats contradict the observed behavior | Verify TTL config and max-entry settings -> Confirm identical tool/input payloads were used -> Inspect cache-key hashing and per-tool scoping -> Check mutation hook invalidation path -> Review expiry cleanup timing and oldest-entry eviction behavior |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/197-access-driven-popularity-scoring.md:19:- Prompt: `Verify access-driven popularity scoring with two comparable memories. Repeatedly retrieve one target memory enough times to push the in-memory access accumulator past the flush threshold, then confirm the persisted access count and last_accessed fields update while a comparable control memory does not. Re-run a ranking query and confirm the more frequently accessed memory receives a stronger popularity contribution. Capture accumulator, flush, ranking, and dormancy evidence and return a concise user-facing pass/fail verdict with the main reason.`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/197-access-driven-popularity-scoring.md:20:- Expected signals: each retrieval increments the in-memory accumulator by 0.1; accumulated access flushes after the threshold is crossed; persisted `access_count` and `last_accessed` update for the hot memory; composite scoring reflects a popularity boost for the more frequently accessed memory; untouched control evidence remains comparatively colder for dormancy analysis\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/11--scoring-and-calibration/197-access-driven-popularity-scoring.md:29:| 197 | Access-driven popularity scoring | Confirm batched access accumulation, thresholded flushes, and popularity-driven ranking effects | `Verify access-driven popularity scoring with two comparable memories. Repeatedly retrieve one target memory enough times to push the in-memory access accumulator past the flush threshold, then confirm the persisted access count and last_accessed fields update while a comparable control memory does not. Re-run a ranking query and confirm the more frequently accessed memory receives a stronger popularity contribution. Capture accumulator, flush, ranking, and dormancy evidence and return a concise user-facing pass/fail verdict with the main reason.` | 1) Prepare or identify two comparable memories that match the same retrieval query 2) Run the shared query once to establish a baseline ranking 3) Retrieve the target memory repeatedly until the accumulator crosses the flush threshold 4) Inspect accumulator state and persisted `access_count` plus `last_accessed` for target vs control 5) Re-run the ranking query and compare popularity-sensitive ordering and dormancy signals | Accumulator rises in 0.1 steps; flush occurs after the threshold is crossed; persisted fields update for the target memory; composite scoring or ranking reflects a popularity boost; colder control memory remains relatively less active for dormancy purposes | Baseline and post-access query results, accumulator snapshots, persisted access metadata, and operator transcript | PASS: target retrievals batch correctly, persistence updates are visible, and the hot memory gains a measurable popularity advantage; FAIL: accumulator does not flush, persisted metadata does not change, or ranking stays indistinguishable from baseline without explanation | Verify repeated retrievals hit the same target memory -> Inspect accumulator threshold and flush path -> Check `access_count` and `last_accessed` persistence writes -> Review composite scoring popularity contribution -> Confirm dormancy logic is reading updated access data |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/165-assistive-reconsolidation-speckit-assistive-reconsolidation.md:20:- Expected signals: similarity >= 0.96 returns 'auto_merge' and archives the older row; 0.88 <= similarity < 0.96 returns 'review' with AssistiveRecommendation logged; similarity < 0.88 returns 'keep_separate'; review tier produces classification (supersede/complement/keep_separate) without destructive action; companion merge guard aborts stale merge attempts with `predecessor_changed` or `predecessor_gone`\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/165-assistive-reconsolidation-speckit-assistive-reconsolidation.md:21:- Pass/fail: PASS if auto-merge triggers at >= 0.96, recommendation logs for review tier, no destructive action occurs for borderline pairs, and predecessor-change detection blocks stale companion merges; FAIL if tier classification is wrong, review tier mutates state, or stale predecessor changes still commit a merge\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/165-assistive-reconsolidation-speckit-assistive-reconsolidation.md:30:| 165 | Assistive reconsolidation (SPECKIT_ASSISTIVE_RECONSOLIDATION) | Verify predecessor change detection in companion reconsolidation path | `Test SPECKIT_ASSISTIVE_RECONSOLIDATION=true with companion reconsolidation safety. Reproduce a merge-eligible predecessor that changes during async embedding generation and capture the evidence needed to prove the shared reconsolidation path returns predecessor_changed or predecessor_gone instead of stale-merging while assistive behavior remains non-destructive. Return a concise user-facing pass/fail verdict with the main reason.` | 1) Enable `SPECKIT_ASSISTIVE_RECONSOLIDATION=true` 2) seed a merge-eligible predecessor used by the companion reconsolidation module 3) begin async merge preparation 4) mutate, archive, or delete the predecessor before transaction re-read 5) verify `predecessor_changed` or `predecessor_gone` is surfaced and no stale merged row is inserted 6) `npx vitest run .opencode/skills/system-spec-kit/mcp_server/tests/reconsolidation.vitest.ts -t \\\\\\\"Aborts merge when predecessor changes during embedding generation\\\\\\\"` | Companion merge path aborts with `predecessor_changed` or `predecessor_gone`; no stale merged row is inserted; assistive layer remains recommendation/shadow-only rather than performing a destructive content merge | Targeted vitest output plus DB evidence showing no merged row was inserted after predecessor mutation | PASS if predecessor mutation blocks the companion merge and assistive behavior remains non-destructive; FAIL if stale merge still commits or assistive layer mutates state outside its documented bounds | Verify predecessor snapshot comparison (`content_hash`, `updated_at`) → Check shared reconsolidation guardrails → Confirm assistive bridge still limits itself to shadow-archive/recommend behavior |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/README.md:111:CocoIndex (semantic search) finds code by concept. Code Graph (structural) maps what connects to what. Startup and recovery surfaces now report freshness-aware graph state, structural read paths return a `readiness` block, and lightly stale graphs may repair inline with bounded `selective_reindex` while empty or broadly stale graphs stay on the explicit `code_graph_scan` path.\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/README.md:540:| `check-template-staleness.sh` | Detect templates that need regeneration                                                        |\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/README.md:932:**Common causes**: The embedding index is stale, or the query is too vague for intent classification.\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/22--context-preservation-and-code-graph/257-working-set-compaction.md:32:  - FAIL: Scoring order incorrect (stale files rank above recent), eviction not triggered, serialization loses data, or merger output missing tracked files\\n/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/manual_testing_playbook/10--graph-signal-activation/081-graph-and-cognitive-memory-fixes.md:19:- Prompt: `Validate graph and cognitive memory fixes. Capture the evidence needed to prove Self-loops prevented; depth clamps enforced; cache invalidation triggers on md:5842:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:66863:- **Recommendation**: adopt now
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296123:2962:208855:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:5884:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:66987:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296129:2968:208861:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6003:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:80046:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296142:2981:208874:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6128:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:86915:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296159:2998:208891:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6245:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:93666:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296175:3014:208907:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6333:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:98710:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296184:3023:208916:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6368:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:99503:    73	Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296189:3028:208921:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6378:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:99703:     9	Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296206:3045:208938:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6465:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:103195:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296217:3056:208949:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6629:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:114892:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296228:3067:208960:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6733:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:121898:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296239:3078:208971:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6828:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:125594:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296245:3084:208977:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6888:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:130836:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296259:3098:208991:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:6986:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:131285:Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296266:3105:208998:.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/005-mempalace/research/iterations/iteration-021.md:7019:/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:132029:    69	Research OpenCode Mnemosyne's hybrid search architecture, plugin design patterns, and compaction survival strategies to identify practical, evidence-backed improvements for `Code_Environment/Public`, especially around combining text and vector search, OpenCode plugin integration, project-vs-global memory scoping, and preserving memory awareness across context compaction. Focus on what the external repo actually proves in `src/index.ts` and what the README describes about the Mnemosyne backend. Classify each recommendation as `adopt now`, `prototype later`, or `reject`.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296624:3464:210494:.opencode/skills/system-spec-kit/manual_testing_playbook/manual_testing_playbook.md:1316:Prompt: `Validate PI-B3 folder description discovery. Capture the evidence needed to prove description.json exists after create.sh; stale detection triggers on spec.md edit; per-folder files preferred over spec.md fallback; mixed-mode aggregation works; invalid JSON or schema-invalid description.json files are ignored, spec.md fallback is used, and existing files are repaired in place; missing description.json falls back cleanly without implicit backfill; out-of-base or prefix-bypass paths are rejected by realpath containment checks; YAML frontmatter is stripped before description extraction, including CRLF-heavy frontmatter cases; memory_context uses folder routing; regeneration leaves valid JSON on disk with no leftover temp files. Return a concise user-facing pass/fail verdict with the main reason.`
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296625:3465:210495:.opencode/skills/system-spec-kit/manual_testing_playbook/manual_testing_playbook.md:1318:description.json exists after create.sh; stale detection triggers on spec.md edit; per-folder files preferred over spec.md fallback; mixed-mode aggregation works; invalid JSON or schema-invalid description.json files are ignored, spec.md fallback is used, and existing files are repaired in place; missing description.json falls back cleanly without implicit backfill; out-of-base or prefix-bypass paths are rejected by realpath containment checks; YAML frontmatter is stripped before description extraction, including CRLF-heavy frontmatter cases; memory_context uses folder routing; regeneration leaves valid JSON on disk with no leftover temp files
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296638:3478:210889:.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/004-opencode-mnemosyne-main/research/research.md:296639:3479:210892:.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/004-opencode-mnemosyne-main/research/research.md:296642:3482:211042:.opencode/skills/system-spec-kit/manual_testing_playbook/14--pipeline-architecture/095-strict-zod-schema-validation-p0-1.md:29:| 095 | Strict Zod schema validation (P0-1) | Confirm schema enforcement rejects hallucinated params | `Validate SPECKIT_STRICT_SCHEMAS enforcement. Capture the evidence needed to prove Zod strict error returned for unknown params in strict mode; extra params pass through in permissive mode; validation occurs per-tool in handler layer. Return a concise user-facing pass/fail verdict with the main reason.` | 1) call any MCP tool with an extra unknown parameter (e.g., `memory_search({query:"test", bogus:1})`) 2) verify Zod strict error is returned 3) set `SPECKIT_STRICT_SCHEMAS=false` and confirm `.passthrough()` allows the extra param 4) verify validation runs per-tool in handler, not duplicated at server dispatch | Zod strict error returned for unknown params in strict mode; extra params pass through in permissive mode; validation occurs per-tool in handler layer | Tool outputs + Zod error messages | PASS if strict mode rejects unknown params and passthrough mode allows them | Inspect `tool-schemas.ts` for `.strict()` vs `.passthrough()` branching |
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296657:3497:211554:.opencode/skills/system-spec-kit/manual_testing_playbook/13--memory-quality-and-indexing/133-dry-run-preflight-for-memory-save.md:29:| 133 | Dry-run preflight for memory_save | Confirm dry-run previews preflight plus semantic insufficiency without indexing side effects | `Validate memory_save dryRun preview behavior, including insufficiency detection. Capture the evidence needed to prove Dry-run returns preflight plus quality-loop and sufficiency payloads; thin memories report INSUFFICIENT_CONTEXT_ABORT without indexing/database mutation; force:true does not bypass insufficiency; rich non-dry-run save indexes the same file. Return a concise user-facing pass/fail verdict with the main reason.` | 1) Create a rich sandbox memory file and a thin sandbox memory file 2) `memory_stats()` and capture baseline totals 3) `memory_save({filePath:"<thin-sandbox-file>", dryRun:true})` and verify preflight details, `qualityLoop`, `sufficiency`, and `rejectionCode:"INSUFFICIENT_CONTEXT_ABORT"` 4) `memory_stats()` and `memory_search({query:"<thin title>"})` to verify no new indexed record from dry-run 5) `memory_save({filePath:"<thin-sandbox-file>", force:true})` and verify it still rejects before indexing 6) `memory_save({filePath:"<rich-sandbox-file>", dryRun:true})` and verify `would_pass:true` with no side effects 7) `memory_save({filePath:"<rich-sandbox-file>", dryRun:false})` and verify the memory becomes searchable | Dry-run returns preflight plus quality-loop and sufficiency payloads; thin memories report `INSUFFICIENT_CONTEXT_ABORT` without indexing/database mutation; `force:true` does not bypass insufficiency; rich non-dry-run save indexes the same file | Dry-run responses for thin and rich files + before/after stats + search outputs + non-dry-run save output | PASS if dry-run surfaces sufficiency explicitly with no index mutation, forced thin save still rejects, and rich non-dry-run save makes the record searchable | Inspect `handlers/memory-save.ts` dryRun and insufficiency branches, `shared/parsing/memory-sufficiency.ts`, `handlers/quality-loop.ts`, and `lib/validation/preflight.ts` |
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296665:3505:212117:.opencode/skills/system-spec-kit/manual_testing_playbook/02--mutation/006-memory-indexing-memory-save.md:29:| EX-006 | Memory indexing (memory_save) | New memory ingestion | `Index memory file and report action. Capture the evidence needed to prove Save action reported; searchable result appears; no template-contract or insufficiency rejection. Return a concise user-facing pass/fail verdict with the main reason.` | `memory_save(filePath)` -> `memory_stats()` -> `memory_search(title)` | Save action reported; searchable result appears; no template-contract or insufficiency rejection | Save output + follow-up search | PASS if indexed and retrievable and the save does not report `INSUFFICIENT_CONTEXT_ABORT` or template-contract failure | Validate file path/type, rendered anchor/frontmatter shape, and content quality |
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296674:3514:212727:.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/004-opencode-mnemosyne-main/research/research.md:296719:3722:223693:.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/004-opencode-mnemosyne-main/research/research.md:296726:3733:225502:.opencode/skills/system-spec-kit/manual_testing_playbook/manual_testing_playbook.md:1690:Expired rows excluded; result limits respected; invalid embeddings rejected cleanly; partial state counted
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:296791:4149:239394:.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/004-opencode-mnemosyne-main/research/research.md:296856:4370:255719:.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/004-opencode-mnemosyne-main/research/research.md:297933:12236:    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/004-opencode-mnemosyne-main/research/research.md:297934:13019:.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/004-opencode-mnemosyne-main/research/research.md:297983:   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/004-opencode-mnemosyne-main/research/research.md:298018:   517	    rerank = true, // Enable reranking by default for better result quality
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298055:   554	        tool: 'memory_search',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298067:   566	      tool: 'memory_search',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298095:   594	          tool: 'memory_search',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298114:   613	      tool: 'memory_search',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298126:   625	      tool: 'memory_search',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298243:   742	    rerank,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298252:   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/004-opencode-mnemosyne-main/research/research.md:298264:   763	    // Wait for embedding model only on cache miss
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298296:   795	      rerank,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298369:     4	// Combines vector, FTS, and BM25 search with fallback
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298378:    13	import { applyMMR } from '@spec-kit/shared/algorithms/mmr-reranker';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298391:    26	import { rerankLocal } from './local-reranker.js';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298427:    62	import type { MMRCandidate } from '@spec-kit/shared/algorithms/mmr-reranker';
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298436:    71	  embedding: Float32Array | number[],
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298482:   117	   * - `'vector'` — cosine similarity from sqlite-vec (normalized from 0-100 to 0-1)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298483:   118	   * - `'bm25'` — BM25 term-frequency relevance (min-max normalized per source group)
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298599:   234	/** Primary vector similarity floor for hybrid fallback passes (percentage units). */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298601:   236	/** Secondary vector similarity floor for adaptive retry passes (percentage units). */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298603:   238	/** Tier-2 vector similarity floor for quality-aware fallback (percentage units). */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298606:   241	/** Minimum MMR candidates required for diversity reranking to be worthwhile. */
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298625:   260	let vectorSearchFn: VectorSearchFn | null = null;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298668:   303	 * Initialize hybrid search with database, vector search, and optional graph search dependencies.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298670:   305	 * @param vectorFn - Optional vector search function for semantic similarity.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298675:   310	  vectorFn: VectorSearchFn | null = null,
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298679:   314	  vectorSearchFn = vectorFn;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298683:   318	// 8. BM25 SEARCH
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298705:  1815	- **What it does**: Mnemosyne’s wrapper forwards search requests to a backend whose BM25/vector/RRF internals are only README-documented, while Public already runs a visible multi-stage hybrid search pipeline.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298720:  1830	- **Why it matters for us**: The behavioral pattern is good, but the wording must point to `session_bootstrap`, `memory_context`, governed saves, and careful deletions instead of cheap direct CLI mutations.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298746:  1856	- **Source**: [external/src/index.ts:140](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/external/src/index.ts#L140), [external/README.md:57](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/external/README.md#L57), [vector-index-store.ts:609](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L609), [memory-crud-update.ts:67](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts#L67); evidence: both
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298762:  1872	- **Why it matters for us**: If we build a native facade, it must delegate to MCP for save/search/recovery and keep CocoIndex/code-graph as separate retrieval planes, or it will become a second authority layer.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298815:  1925	- **What it does**: Mnemosyne’s wrapper forwards search requests to a backend whose BM25/vector/RRF internals are only README-documented, while Public already runs a visible multi-stage hybrid search pipeline.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298830:  1940	- **Why it matters for us**: The behavioral pattern is good, but the wording must point to `session_bootstrap`, `memory_context`, governed saves, and careful deletions instead of cheap direct CLI mutations.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298856:  1966	- **Source**: [external/src/index.ts:140](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/external/src/index.ts#L140), [external/README.md:57](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/999-hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/external/README.md#L57), [vector-index-store.ts:609](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.ts#L609), [memory-crud-update.ts:67](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts#L67); evidence: both
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298872:  1982	- **Why it matters for us**: If we build a native facade, it must delegate to MCP for save/search/recovery and keep CocoIndex/code-graph as separate retrieval planes, or it will become a second authority layer.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:298945:/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/004-opencode-mnemosyne-main/research/research.md:298947:/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/004-opencode-mnemosyne-main/research/research.md:299464:    84	  const database = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299477:    97	      deletedCount = vectorIndex.deleteMemory(numericId) ? 1 : 0;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299521:   141	    const memories: { id: number }[] = vectorIndex.getMemoriesByFolder(specFolder as string);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299572:    75	  const existing = vectorIndex.getMemory(id);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299577:    80	  const database = vectorIndex.getDb();
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299586:    89	  let embeddingRegenerated = false;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299587:    90	  let embeddingMarkedForReindex = false;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299588:    91	  let embeddingStatusNeedsPendingWrite = false;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299592:    95	    console.error(`[memory-update] Title changed, regenerating embedding for memory ${id} [requestId=${requestId}]`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299597:   100	      // This produces better semantic embeddings that capture the full memory context.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299599:   102	      const embeddingInput = contentText ? `${title}\n\n${contentText}` : title;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299600:   103	      newEmbedding = await embeddings.generateDocumentEmbedding(embeddingInput);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299605:   108	        embeddingStatusNeedsPendingWrite = true;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299606:   109	        embeddingMarkedForReindex = true;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299618:   121	      updateParams.embedding = newEmbedding;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299619:   122	      embeddingRegenerated = true;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299620:   123	    } else if (!embeddingMarkedForReindex) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299623:   126	        embeddingStatusNeedsPendingWrite = true;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299624:   127	        embeddingMarkedForReindex = true;
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299628:   131	          'Failed to regenerate embedding (null result), update rolled back. No changes were made.',
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299636:   139	  // Cache invalidation, BM25 re-index, ledger append) in a single transaction for atomicity.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299638:   141	  const fields = Object.keys(updateParams).filter((key) => key !== 'id' && key !== 'embedding');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299642:   145	      if (embeddingStatusNeedsPendingWrite) {
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299643:   146	        vectorIndex.updateEmbeddingStatus(id, 'pending');
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299646:   149	      vectorIndex.updateMemory(updateParams);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299648:   151	      // T2-6 — BM25 index stores title + trigger phrases; must re-index when either changes
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299650:   153	      // T-05: BM25 re-index failure now rolls back the transaction when the index is operational.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299651:   154	      // Infrastructure failures (BM25 not available, DB missing prepare) are non-fatal warnings.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299667:   170	          // Infrastructure failures mean the BM25 subsystem is unavailable or torn down —
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299678:   181	            console.warn(`[memory-crud-update] BM25 infrastructure unavailable, skipping re-index [requestId=${requestId}]: ${bm25ErrMsg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299680:   183	            console.error(`[memory-crud-update] BM25 re-index failed, rolling back update [requestId=${requestId}]: ${bm25ErrMsg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299681:   184	            throw new Error(`BM25 re-index failed: ${bm25ErrMsg}`);
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299813:- **Why it matters**: The pattern is good, but the verbs must be `session_bootstrap`, `memory_context`, governed save flows, and careful revision, not raw add/delete habits.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299841:- **Why it matters**: A facade could improve DX, but it must delegate to MCP and preserve separate memory, CocoIndex, and code-graph authorities.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299847:- **What it does**: Mnemosyne documents hybrid retrieval; Public already implements visible vector/FTS/BM25/RRF-style hybrid search in-process.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299878:2. rewrite startup and AGENTS-style guidance in Public terms around `session_bootstrap`, `memory_context`, and governed save/update/delete flows.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299955:- **Why it matters**: The pattern is good, but the verbs must be `session_bootstrap`, `memory_context`, governed save flows, and careful revision, not raw add/delete habits.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299983:- **Why it matters**: A facade could improve DX, but it must delegate to MCP and preserve separate memory, CocoIndex, and code-graph authorities.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:299989:- **What it does**: Mnemosyne documents hybrid retrieval; Public already implements visible vector/FTS/BM25/RRF-style hybrid search in-process.
./.opencode/specs/system-spec-kit/z_future/hybrid-rag-fusion-upgrade/001-research-hybrid-rag-fusion-systems/004-opencode-mnemosyne-main/research/research.md:300020:2. rewrite startup and AGENTS-style guidance in Public terms around `session_bootstrap`, `memory_context`, and governed save/update/delete flows.

codex
The broad scan confirmed this repo has three related retrieval planes: Spec Kit Memory search, Code Graph, and CocoIndex. I’m narrowing now to the implementation files and specs that explain the routing, because the raw search space is enormous.
exec
/bin/zsh -lc "rg --files .opencode/skills/system-spec-kit/mcp_server | rg 'search|retriev|rerank|vector|bm25|fts|coco|graph|tool-schemas|handlers'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/handlers/index.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/handlers/advisor-status.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/handlers/advisor-validate.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/handlers/advisor-recommend.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/lib/scorer/lanes/graph-causal.ts
.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts
.opencode/skills/system-spec-kit/mcp_server/plugin_bridges/spec-kit-compact-code-graph-bridge.mjs
.opencode/skills/system-spec-kit/mcp_server/code_graph/README.md
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/query.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/index.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/README.md
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-reindex.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/context.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/detect-changes.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/scan.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-feedback.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/verify.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/status.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/handlers/ccc-status.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/phase-runner.test.ts
.opencode/skills/system-spec-kit/mcp_server/formatters/search-results.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/detect-changes.test.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-seed-resolver.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-scan.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/edge-metadata-sanitize.test.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill-graph.json
.opencode/skills/system-spec-kit/mcp_server/configs/search-weights.json
.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/code_graph/tools/code-graph-tools.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tools/index.ts
.opencode/skills/system-spec-kit/mcp_server/lib/interfaces/vector-store.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/init-skill-graph.sh
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/assets/code-graph-gold-queries.json
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-query-handler.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-ops-hardening.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-siblings-readiness.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-verify.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-context-handler.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/code-graph-indexer.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/tests/edge-drift.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/code-graph-context.ts
.opencode/skills/system-spec-kit/mcp_server/api/search.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/ops-hardening.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/seed-resolver.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/compact-merger.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-result-adapter.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/startup-brief.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/README.md
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/working-set-tracker.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/edge-drift.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/query-intent-classifier.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/readiness-contract.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/tree-sitter-parser.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/indexer-types.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/pe-gating.ts
.opencode/skills/system-spec-kit/mcp_server/tools/skill-graph-tools.ts
.opencode/skills/system-spec-kit/mcp_server/lib/utils/cocoindex-path.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/utils/workspace-path.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-utils.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/v-rule-bridge.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index-alias.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/chunking-orchestrator.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-save.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-stats.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/budget-allocator.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/structural-indexer.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/gold-query-verifier.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/runtime-detection.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/ensure-ready.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/diff-parser.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/phase-runner.ts
.opencode/skills/system-spec-kit/mcp_server/code_graph/lib/index.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/scripts/skill_graph_compiler.py
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-health.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/types.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/checkpoints.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/causal-links-processor.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/README.md
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index-discovery.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/session-learning.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/handler-utils.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/causal-graph.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-types.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-ingest.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-bulk-delete.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-triggers.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud.ts
.opencode/skills/system-spec-kit/mcp_server/lib/skill-graph/skill-graph-queries.ts
.opencode/skills/system-spec-kit/mcp_server/lib/skill-graph/skill-graph-db.ts
.opencode/skills/system-spec-kit/mcp_server/tests/reranker-eval-comparison.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/schemas/advisor-tool-schemas.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/eval-reporting.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-index.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/quality-loop.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/session-bootstrap.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/mutation-hooks.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-list.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/session-health.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-update.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/session-resume.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/index.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/memory-crud-delete.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/skill-graph/query.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/skill-graph/index.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/skill-graph/validate.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/skill-graph/scan.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/skill-graph/status.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/community-storage.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/convergence.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-schema.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/contradiction-detection.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-metadata-parser.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/community-detection.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/graph-signals.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/README.md
.opencode/skills/system-spec-kit/mcp_server/lib/graph/usage-tracking.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/usage-ranking-signal.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/community-summaries.ts
.opencode/skills/system-spec-kit/mcp_server/lib/graph/temporal-edges.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/query.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/index.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/README.md
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/upsert.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/coverage-graph/status.ts
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph-regression-flag-off.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/sparse-first-graph.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/skill-graph-handlers.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/search-extended.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/retrieval-directives.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-benchmark-memory-search.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/search-flags.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph-lifecycle.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/community-search.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph-flags.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/db-helpers.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/spec-folder-mutex.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/index.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/atomic-index-memory.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/create-record.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/embedding-pipeline.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/types.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/README.md
.opencode/skills/system-spec-kit/mcp_server/handlers/save/reconsolidation-bridge.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/markdown-evidence-builder.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/dedup.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/post-insert.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/response-builder.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/validation-responses.ts
.opencode/skills/system-spec-kit/mcp_server/handlers/save/pe-orchestration.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph-first-routing-nudge.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/retrieval-trace.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/README.md
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-query.ts
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-signals.ts
.opencode/skills/system-spec-kit/mcp_server/lib/coverage-graph/coverage-graph-db.ts
.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-context-headers.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/bm25-security.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/integration-causal-graph.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-db.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/archive/coverage-graph-tools.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph-metadata-schema.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph-roadmap-finalization.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/search-limits-scoring.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/recovery-payload.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph/graph-metadata-lineage.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/mmr-reranker.vitest.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/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/folder-discovery.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-schema.ts
.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-eval-channels.vitest.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/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/causal-boost.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-flags.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/cross-encoder.ts
.opencode/skills/system-spec-kit/mcp_server/lib/eval/bm25-baseline.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/telemetry/retrieval-telemetry.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/skill_advisor/graph-metadata.json
.opencode/skills/system-spec-kit/mcp_server/tests/gate-d-regression-embedding-semantic-search.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-impl.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/graph-scoring-integration.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/sqlite-fts.vitest.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/tfidf-summarizer.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md
.opencode/skills/system-spec-kit/mcp_server/lib/search/dynamic-token-budget.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/search-utils.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/confidence-scoring.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/entity-linker.ts
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.opencode/skills/system-spec-kit/mcp_server/lib/search/anchor-metadata.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-store.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/query-router.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/encoding-intent.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/intent-classifier.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-lifecycle.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/reranker.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/surrogate-storage.ts
.opencode/skills/system-spec-kit/mcp_server/tests/stage3-rerank-regression.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/reranker.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/feedback-denylist.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/vector-index-types.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/session-boost.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/graph-flags.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/evidence-gap-detector.ts
.opencode/skills/system-spec-kit/mcp_server/lib/search/confidence-truncation.ts
.opencode/skills/system-spec-kit/mcp_server/tests/deep-loop-graph-query.vitest.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/learned-feedback.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/skill-graph-db.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/skill_advisor/tests/handlers/advisor-recommend.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/handlers/advisor-validate.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/skill_advisor/tests/legacy/advisor-graph-health.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/coverage-graph-signals.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/hybrid-search-flags.vitest.ts
.opencode/skills/system-spec-kit/mcp_server/tests/local-reranker.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/handler-causal-graph.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/memory-search-integration.vitest.ts
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.opencode/skills/system-spec-kit/mcp_server/tests/vector-index-store.vitest.ts
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exec
/bin/zsh -lc "rg -n \"hybrid search|Graph-first|graph-first|CocoIndex|memory_search|memory_context|BM25|FTS5|RRF|rerank|Search Pipeline|five core channels\" README.md .opencode/README.md .opencode/skills/system-spec-kit/SKILL.md .opencode/commands/memory/search.md .opencode/skills/mcp-coco-index/SKILL.md --glob '"'!node_modules/**'"'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
.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:10:# CocoIndex Code - Semantic Code Search via Vector Embeddings
.opencode/skills/mcp-coco-index/SKILL.md:187:CocoIndex Code provides two access patterns for semantic code search:
.opencode/skills/mcp-coco-index/SKILL.md:192:### CLI Approach (Primary) - CocoIndex Code CLI
.opencode/skills/mcp-coco-index/SKILL.md:245:CocoIndex Code supports two embedding models, configured via `~/.cocoindex_code/global_settings.yml`:
.opencode/skills/mcp-coco-index/SKILL.md:258:CocoIndex Code resolves the project root in this order:
.opencode/skills/mcp-coco-index/SKILL.md:267:The CocoIndex Code daemon manages background indexing and serves search requests:
.opencode/skills/mcp-coco-index/SKILL.md:455: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:459:| `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:460:| `ccc_status` | Spec Kit Memory | Check CocoIndex availability and index stats | none |
.opencode/skills/mcp-coco-index/SKILL.md:466:> **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:470:CocoIndex Code supports 28+ languages with language-aware chunk splitting:
.opencode/skills/mcp-coco-index/SKILL.md:568:- CocoIndex Code handles code search; Code Mode handles external APIs
.opencode/skills/mcp-coco-index/SKILL.md:582:**CocoIndex Code (ccc)**:
.opencode/skills/mcp-coco-index/SKILL.md:598:| **install.sh** | Install CocoIndex  | `bash .opencode/skills/mcp-coco-index/scripts/install.sh`                  |
.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:102:The unified context tool runs a hybrid retrieval pipeline with **graph-first routing** (026):
.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: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`)
.opencode/commands/memory/search.md: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
.opencode/commands/memory/search.md:111:- `getRerankerStatus()` exposes reranker latency plus cache `hits`, `misses`, `staleHits`, and `evictions`
.opencode/commands/memory/search.md:290:spec_kit_memory_memory_context({
.opencode/commands/memory/search.md:391:**memory_context L1 Budget:** ~2000 tokens total (mode-managed)
.opencode/commands/memory/search.md:734:| `mode` | string | No | Evaluation mode. Defaults to `ablation`; use `k_sensitivity` for raw pre-fusion RRF K analysis |
.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: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:890:spec_kit_memory_memory_search({
.opencode/commands/memory/search.md:921:| 1 | `memory_context` | L1 | Retrieval | (default) |
.opencode/commands/memory/search.md:923:| 3 | `memory_search` | 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:974:| `rerank` | boolean | true | Enable cross-encoder reranking |
.opencode/commands/memory/search.md:975:| `applyLengthPenalty` | boolean | true | Compatibility-only reranker option. Current runtime keeps it on the surface, but the length multiplier is always `1.0` so no documents are penalized for size |
.opencode/README.md:45:1. **Memory Engine**: 47 MCP tools across 7 layers, with graph-first structural routing (Code Graph before semantic), 3-tier FTS fallback, 3-source indexing, 7-intent retrieval routing, schema v15 metadata (`document_type`, `spec_level`), document-type scoring, causal lineage tracking, typed-weighted degree channel, persistent embedding cache, query complexity routing, RSF fusion, confidence truncation, post-save quality gates with heuristic calibration, and CocoIndex semantic code search bridge
.opencode/README.md:54:| MCP Servers | 4 | Spec Kit Memory, CocoIndex Code, Code Mode, Sequential Thinking |
.opencode/README.md:55:| MCP Tools | 56 | 47 memory + 7 code mode + 1 CocoIndex + 1 sequential thinking |
.opencode/README.md:255:- **Retrieval:** Graph-first routing (structural Code Graph before semantic CocoIndex), hybrid search across vector, BM25, FTS5, trigger matching and typed-weighted degree channels with RRF + RSF (Reciprocal Similarity Fusion) fusion, 3-tier FTS fallback (FTS5 full-text -> BM25 keyword scoring -> Grep/Glob filesystem search when graph and semantic channels miss), cross-encoder reranking, query complexity routing (simple/moderate/complex), confidence truncation (2x median gap), persistent embedding cache and interference scoring
.opencode/README.md:259:- **Features:** Constitutional tier, session deduplication, causal lineage tracking, temporal decay, learning analytics, typed retrieval contracts, artifact-class routing, adaptive fusion, append-only mutation ledger, extended retrieval telemetry, session-cognitive automation (attention-based decay, tiered content injection, co-activation of related memories), persistent embedding cache (SQLite `embedding_cache` table), interference scoring (TM-01 penalty), classification-based decay (TM-03 context-type + importance-tier multipliers), query complexity routing (simple/moderate/complex tier dispatch), RSF fusion (single-pair, multi-list, cross-variant alternatives to RRF), channel min-representation (QUALITY_FLOOR=0.2), confidence truncation (2x median gap, min 3 results), dynamic token budget (1500/2500/4000 by tier), cold-start N4 boost, min-max score normalization, co-activation fan-effect (sqrt divisor), CORRECTION/PREFERENCE signal categories, pre-flight token budget estimation, verify-fix-verify quality loop, spec folder description discovery, post-save quality gates (structure/semantic/duplicate with heuristic calibration and trigger sanitization), graph-first structural routing (Code Graph -> CocoIndex -> Memory), 3-tier FTS fallback chain (PI-A2), CocoIndex semantic code search bridge, and ~14 `SPECKIT_*` feature flags
.opencode/README.md:266:**Unified Entry Point:** `memory_context()` provides intent-aware routing with 7 intents: `add_feature`, `fix_bug`, `understand`, `refactor`, `security_audit`, `find_spec`, `find_decision`.
.opencode/README.md:334:- **Research task:** `memory_match_triggers()`, `memory_context()`, Document findings
.opencode/skills/system-spec-kit/SKILL.md:566:Context preservation across sessions via 5-channel hybrid retrieval (vector, FTS5, BM25, graph, and degree) with Reciprocal Rank Fusion, intent-aware routing, and post-fusion reranking/filtering.
.opencode/skills/system-spec-kit/SKILL.md:576:| `memory_context()`              | L1    | Unified entry point - modes: auto, quick, deep, focused, resume |
.opencode/skills/system-spec-kit/SKILL.md:577:| `memory_search()`               | L2    | 5-channel hybrid retrieval with intent-aware routing, channel normalization, graph/degree signals, reranking, and filtered output |
.opencode/skills/system-spec-kit/SKILL.md:591:> **Search architecture:** The search pipeline uses a 4-stage architecture (candidate generation → fusion → reranking → filtering). Current retrieval uses five channels, normalizes fallback thresholds correctly, keeps disabled channels disabled through fallback, defers irreversible confidence truncation until after reranking, and enforces token budgets using actual post-truncation counts. Adaptive fusion includes an internal continuity profile (`semantic 0.52`, `keyword 0.18`, `recency 0.07`, `graph 0.23`), Stage 3 uses a minimum rerank gate of 4 candidates, the retained `applyLengthPenalty` input is a compatibility no-op, and `getRerankerStatus()` exposes reranker cache hits, misses, stale hits, and evictions. See [search/README.md](./mcp_server/lib/search/README.md) for pipeline details, scoring algorithms, and graph signal features.
.opencode/skills/system-spec-kit/SKILL.md:593:**memory_context() - Mode Routing:**
.opencode/skills/system-spec-kit/SKILL.md:602:**memory_search() - Key Rules:**
.opencode/skills/system-spec-kit/SKILL.md:632:- **Adaptive fusion** - Intent-aware weighted RRF with the 7 public task-type profiles (fix_bug, add_feature, understand, refactor, security_audit, find_spec, find_decision) plus the internal continuity profile used for resume-oriented retrieval, along with corrected channel fallback and normalization behavior in the live hybrid pipeline
.opencode/skills/system-spec-kit/SKILL.md:647:- **Memory causal trust display badges (012/005)** - `memory_search` results now carry an additive `trustBadges` payload per `MemoryResultEnvelope`: `confidence` from edge `strength`, `extractionAge`, `lastAccessAge`, `orphan` (no incoming edges), `weightHistoryChanged` (any connected edge has a `weight_history` row). Display-only — derived at response time from existing causal-edge columns; no schema change, no new relation types, no new storage of code/process/tool facts. Response profiles (`quick`, `research`, `resume`) preserve the badge payload on `results[]` and `topResult` (ADR-012-005)
.opencode/skills/system-spec-kit/SKILL.md:656:| `SPECKIT_ADAPTIVE_FUSION`     | on      | Enables intent-aware weighted RRF in `memory_search()`, including the internal continuity profile used for resume-style retrieval (set `false` to disable) |
.opencode/skills/system-spec-kit/SKILL.md:682:| `SPECKIT_RRF_K_EXPERIMENTAL` | on      | Per-intent NDCG@10-maximizing K selection over sweep grid |
.opencode/skills/system-spec-kit/SKILL.md:751:**Claude lifecycle flow:** `UserPromptSubmit` covers prompt-time advisor delivery. `PreCompact -> SessionStart(compact)` handles cached context reinjection. On startup, the shared snapshot covers memory continuity, code-graph state, CocoIndex availability, and an explicit note that later structural reads may differ if the repo state changed. On resume, the runtime loads prior session state.
.opencode/skills/system-spec-kit/SKILL.md:775:**Architecture:** CocoIndex (semantic, external MCP) finds code by concept. Code Graph (structural, this system) maps imports, calls, hierarchy. Memory (session, existing MCP) preserves decisions. The compact-merger combines all three under a 4000-token budget for compaction injection.
.opencode/skills/system-spec-kit/SKILL.md:789:**Context metadata:** `code_graph_context` success payloads carry structured `data.metadata.partialOutput` (`isPartial`, `reasons`, `omittedSections`, `omittedAnchors`, `truncatedText`) plus an explicit `deadlineMs` field so callers can distinguish a complete answer from one trimmed by deadline or budget pressure. `code_graph_status` exposes `graphQualitySummary` (detector provenance + edge-enrichment confidence). CocoIndex seed fidelity preserves `score`, `snippet`, and range metadata through context resolution.
.opencode/skills/system-spec-kit/SKILL.md:797:**Query routing:** Structural queries (callers, imports, deps) -> `code_graph_query`. Semantic/concept queries -> CocoIndex (`mcp__cocoindex_code__search`). Session/memory queries -> `memory_context`.
.opencode/skills/system-spec-kit/SKILL.md:799:**CocoIndex seed bridge:** CocoIndex search results (file + line range) are accepted as seeds by `code_graph_context`, which resolves them to graph nodes and expands structurally. This combines "what resembles what" (CocoIndex) with "what connects to what" (Code Graph).
.opencode/skills/system-spec-kit/SKILL.md:801:**CCC tools** (CocoIndex lifecycle):
.opencode/skills/system-spec-kit/SKILL.md:805:| `ccc_status` | Check CocoIndex availability and index status |
.opencode/skills/system-spec-kit/SKILL.md:806:| `ccc_reindex` | Trigger incremental or full CocoIndex re-indexing |
.opencode/skills/system-spec-kit/SKILL.md:814:| `session_resume` | Combined memory + code graph + CocoIndex resume in one call |
README.md:56:| **🔧 60 MCP Tools** | spec_kit_memory (51), code mode (7), CocoIndex (1), sequential thinking (1) — see canonical count in FAQ |
README.md:57:| **🔍 CocoIndex Code** | Semantic code search via vector embeddings - natural-language discovery across 28+ languages |
README.md:58:| **🏗️ Code Graph** | Structural indexer + SQLite - call graphs, imports, hierarchy, LLM-oriented neighborhoods, graph-first routing |
README.md:90:         │  5 core + CocoIndex bridge: Vector,      │
README.md:91:         │  BM25, FTS5, Causal Graph, Degree        │
README.md:92:         │  Graph-first routing ─ 3-tier fallback    │
README.md:93:         │  FSRS decay ─ RRF fusion ─ query intel   │
README.md:336:The Memory Engine is a local-first cognitive memory system built as an MCP server. `generate-context.js` updates canonical packet continuity and may emit supporting generated context artifacts inside the spec folder. Canonical continuity lives in the spec packet itself: use `/spec_kit:resume` as the recovery surface, then rebuild context in this order: `handover.md` -> `_memory.continuity` -> canonical spec docs. The MCP server indexes those packet-local sources with vector embeddings, BM25 and FTS5 full-text search, and `memory_match_triggers()` can still surface relevant prior context automatically when deeper retrieval is needed.
README.md:357:| **L7** | Maintenance | 10 | 1,000 | Index scans, async ingest, learning history, and graph/CocoIndex maintenance |
README.md:365:Every search checks five core channels at once, with CocoIndex available as a semantic code search bridge:
README.md:368:- **FTS5** - Full-text search on exact words and phrases.
README.md:369:- **BM25** - Keyword relevance scoring.
README.md:373:**Reciprocal Rank Fusion (RRF)** combines results across channels so memories scoring well in multiple channels rise to the top. **Graph-first routing** dispatches structural queries to the Code Graph first, then CocoIndex for semantic code discovery, then the memory pipeline. A **3-tier FTS fallback** activates when graph and semantic channels miss: FTS5 full-text, BM25 keyword scoring, then Grep/Glob filesystem search. The system truncates weak results and ensures every active channel is represented.
README.md:376:#### Search Pipeline
README.md:381:- **Fusion** - RRF-based scoring with post-fusion signals such as co-activation, FSRS decay, interference control, intent weights, and graph/session boosts when enabled.
README.md:382:- **Rerank** - Cross-encoder reranking with chunk reassembly, a minimum Stage 3 gate of 4 candidates, and compatibility-only length-penalty wiring that resolves to a neutral `1.0` multiplier. `getRerankerStatus()` exposes latency plus cache hits, misses, stale hits, and evictions; if the reranker is unavailable, Stage 2 order is preserved with degraded metadata.
README.md:383:- **Filtering** - State/quality filtering, confidence annotation, token-budget enforcement, and final response shaping without mutating post-rerank scores.
README.md:508:### 🔍 CocoIndex + Code Graph
README.md:510:The framework uses two different code-understanding systems on purpose. **CocoIndex** handles semantic discovery, so the assistant can answer "find code that does X" or "how is Y implemented?" without knowing exact symbols first. The **Code Graph** handles structural expansion, so the assistant can answer questions like "what calls this?", "what imports this?", or "what breaks if we change it?" using an indexed relationship graph.
README.md:512:The intended routing order is graph-first: the code graph resolves structural queries first, CocoIndex finds semantic candidates when structural resolution misses, and Memory supports session decisions and active-task context after the packet-local recovery sources have been checked. A 3-tier FTS fallback escalates automatically when results are weak.
README.md:566:| **CocoIndex** | Concept search, similar implementations, unfamiliar modules | `mcp__cocoindex_code__search` |
README.md:569:| **CCC utilities** | CocoIndex availability, reindexing, result feedback | `ccc_status`, `ccc_reindex`, `ccc_feedback` |
README.md:574:The default routing order is: **Code Graph** (structural) -> **CocoIndex** (semantic code) -> **Memory** (session/decision context). This graph-first approach tries structural resolution before semantic similarity, with a 3-tier FTS fallback when earlier stages miss.
README.md:577:- Use **CocoIndex** for semantic and intent-based questions: "find code that validates memory quality", "show similar routing patterns", "where is the logic for X?"
README.md:832:- Search order: `match_triggers` → `memory_context` → `memory_search` → grep/glob
README.md:834:- Uses both CocoIndex semantic search and the 5-channel memory system. Read-only.
README.md:1078:- Diagnoses all 4 MCP servers (Spec Kit Memory, CocoIndex Code, Code Mode, Sequential Thinking) with PASS/WARN/FAIL per check
README.md:1188:- **Search Pipeline** - 5-channel retrieval, fallback routing, reranking, graph-walk rollout, confidence and token-budget policies.
README.md:1199:The runtime centers on a SQLite `memory_index` table with 56 columns plus companion FTS5/vector, lineage, checkpoint, working-memory, and eval tables.
README.md:1202:- **Search companions** - FTS5 and vector tables support lexical and embedding retrieval alongside BM25 rebuild/index data.
README.md:1259:A: Packet continuity and any supporting generated context artifacts use structured frontmatter and anchored markdown so the memory engine can classify, index, and retrieve them reliably. For recovery, start with `/spec_kit:resume` and the packet-local continuity ladder `handover.md` -> `_memory.continuity` -> canonical spec docs. After that, `memory_match_triggers()` can do a fast trigger/cognitive pass, while `memory_context()` and `memory_search()` handle deeper retrieval with intent routing, reranking, and filtering.
README.md:1279:A: 60 total across 4 native MCP servers, sourced from the registered MCP-dispatched tools only (internal helper handlers and any deferred / not-yet-wired handlers are intentionally excluded). The canonical count for the `spec_kit_memory` server is `TOOL_DEFINITIONS.length` in `.opencode/skills/system-spec-kit/mcp_server/tool-schemas.ts` (currently 51). Breakdown: 51 `spec_kit_memory` tools (3 L1 orchestration + 4 L2 core + 4 L3 discovery + 4 L4 mutation + 4 L5 lifecycle + 8 L6 analysis + 5 L7 maintenance + 5 code graph + 7 skill graph/advisor + 3 CocoIndex bridge + 4 deep loop graph), 7 code mode tools, 1 semantic code search tool (`cocoindex_code`), and 1 sequential thinking tool. All server bindings are defined in `opencode.json`.
README.md:1318:*Documentation version: 4.4 | Last updated: 2026-04-25 | Framework: 12 agents, 21 skills, 23 commands, 60 MCP tools (51 spec_kit_memory + 7 code mode + 1 CocoIndex + 1 sequential thinking; canonical source `TOOL_DEFINITIONS` in `tool-schemas.ts`; deferred / internal-only handlers do NOT count).*

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.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/003-scripts-interop-refactor/implementation-summary.md
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/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/orchestrator.ts | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
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     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;
   181	
   182	  return {
   183	    results: stage4Result.final,
   184	    metadata: {
   185	      stage1: stage1Result.metadata,
   186	      stage2: stage2Result.metadata,
   187	      stage3: stage3Result.metadata,
   188	      stage4: stage4Result.metadata,
   189	      timing,
   190	      degraded: degraded || undefined,
   191	    },
   192	    annotations: stage4Result.annotations,
   193	    trace: config.trace,
   194	  };
   195	}

 succeeded in 0ms:
     1	---
     2	title: "Search Subsystem"
     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."
     4	trigger_phrases:
     5	  - "search subsystem"
     6	  - "hybrid search"
     7	  - "vector search"
     8	---
     9	
    10	# Search Subsystem
    11	
    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.
    13	
    14	---
    15	
    16	## TABLE OF CONTENTS
    17	<!-- ANCHOR:table-of-contents -->
    18	
    19	- [1. OVERVIEW](#1-overview)
    20	  - [4-STAGE PIPELINE ARCHITECTURE](#4-stage-pipeline-architecture)
    21	- [2. KEY CONCEPTS](#2-key-concepts)
    22	- [3. MODULE STRUCTURE](#3-module-structure)
    23	- [4. FEATURES](#4-features)
    24	  - [GRAPH SIGNAL FEATURES](#graph-signal-features)
    25	  - [SAVE-TIME PROCESSING PIPELINE](#save-time-processing-pipeline)
    26	  - [SCORING ENHANCEMENTS](#scoring-enhancements)
    27	- [FTS CAPABILITY CASCADE FLOOR](#fts-capability-cascade-floor)
    28	- [5. USAGE EXAMPLES](#5-usage-examples)
    29	- [6. RECENT CHANGES (SPRINT 8)](#6-recent-changes-sprint-8)
    30	- [7. RELATED RESOURCES](#7-related-resources)
    31	
    32	<!-- /ANCHOR:table-of-contents -->
    33	
    34	---
    35	
    36	## 1. OVERVIEW
    37	<!-- ANCHOR:overview -->
    38	
    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.
    40	
    41	Gate E alignment: retrieval is subordinate to the canonical continuity chain. Resume and continuity work should anchor on `/spec_kit:resume`, then rebuild context from `handover.md -> _memory.continuity -> spec docs`. Search helps rank supporting evidence after those source-of-truth surfaces are known.
    42	
    43	**Core Capabilities:**
    44	- **5-Channel Hybrid Search**: Vector (semantic) + BM25/FTS5 (lexical) + Graph (relationship-based) + Graph Structure (structural)
    45	- **RRF Score Fusion**: Industry-standard k=40 with convergence bonuses
    46	- **Intent Classification**: 7 intent types route to task-specific retrieval weights
    47	- **Query Enhancement**: Fuzzy matching (Levenshtein) + acronym expansions (via hybrid-search.ts inline logic)
    48	- **Reranking Pipeline**: Optional cross-encoder with length penalties
    49	- **MMR Diversity Reranking**: Maximal Marginal Relevance to reduce redundancy in result sets
    50	- **Evidence Gap Detection**: Identifies missing context and suggests follow-up queries
    51	- **Schema Management**: sqlite-vec schema v15 (current) with document-type fields, event-based decay and phase-aware columns
    52	
    53	**Architecture Pattern:**
    54	```text
    55	Query Input
    56	    |
    57	Intent Classifier -> Task-specific weights
    58	    |
    59	Parallel Search (5 channels)
    60	|---> Vector (sqlite-vec)       -> Semantic matches
    61	|---> BM25 (Pure JS)            -> Keyword matches
    62	|---> Graph (Co-activation)     -> Relationship matches
    63	|---> Graph Structure           -> Structural matches
    64	    |
    65	RRF Fusion (k=40) + Adaptive Fusion -> Unified scores
    66	    |
    67	MMR Diversity Reranking -> Redundancy reduction
    68	    |
    69	Cross-Encoder Rerank (optional) -> Relevance refinement
    70	    |
    71	Recency Boost + Co-activation -> Final adjustments
    72	    |
    73	Final Results
    74	```
    75	
    76	**Architecture Note:**
    77	`vector-index.ts` is the primary typed export surface for the vector index and re-exports the split schema, query, mutation, store and alias modules. `vector-index-impl.ts` is now a 14-line backward-compatibility shim that simply re-exports `vector-index.ts` for older import paths.
    78	
    79	<a id="4-stage-pipeline-architecture"></a>
    80	### 4-Stage Pipeline Architecture
    81	
    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`.
    83	
    84	```text
    85	Stage 1                Stage 2                 Stage 3              Stage 4
    86	CANDIDATE GEN    -->   FUSION + SIGNALS   -->  RERANK + AGGREGATE  -->  FILTER + ANNOTATE
    87	(no score changes)     (single scoring point)  (score changes: YES)    (score changes: NO)
    88	```
    89	
    90	**Stage 1 — Candidate Generation** (`stage1-candidate-gen.ts`):
    91	Executes 5 search channels in parallel and collects raw candidates with no scoring modifications.
    92	
    93	| Channel | Source | Description |
    94	|---------|--------|-------------|
    95	| Vector | `vector-index.ts` | Semantic similarity via sqlite-vec through the split vector-index modules |
    96	| BM25 | `bm25-index.ts` | Pure TypeScript keyword matching |
    97	| FTS5 | `sqlite-fts.ts` | SQLite FTS5 BM25 weighted scoring |
    98	| Graph | `graph-search-fn.ts` | Causal edge traversal + typed-weighted degree (R4) |
    99	| Degree | `graph-search-fn.ts` | Structural graph discovery via typed-weighted degree |
   100	
   101	Post-channel: constitutional memory injection, quality score filtering, tier/contextType filtering.
   102	
   103	**Stage 2 — Fusion + Signal Integration** (`stage2-fusion.ts`):
   104	Single authoritative point for ALL scoring signals. Signal application order is fixed:
   105	
   106	1. Session boost — working-memory attention amplification
   107	2. Causal boost — graph-traversal neighbor amplification
   108	3. Community co-retrieval (N2c) — inject community co-members
   109	4. Graph signals (N2a + N2b) — momentum + causal depth
   110	5. Testing effect — FSRS strengthening write-back (opt-in via `trackAccess`)
   111	6. Intent weights — non-hybrid only (G2 double-weighting prevention: `isHybrid` boolean guard)
   112	7. Artifact routing — class-based weight boosts
   113	8. Feedback signals — learned trigger boosts (0.7x weight) + negative demotions
   114	9. Anchor metadata — extract named ANCHOR sections (annotation only)
   115	10. Validation signals — quality scoring multiplier (clamped 0.8-1.2)
   116	
   117	**Stage 3 — Rerank + Aggregate** (`stage3-rerank.ts`):
   118	Cross-encoder reranking (optional, min 2 results) followed by MPAB chunk-to-memory aggregation. Aggregation formula: `parentScore = sMax + 0.3 * Sum(rest) / sqrt(N)` where `sMax` is the best chunk score and N is the remaining chunk count. Chunk ordering preserves `chunk_index` document order (B2 guarantee). `contentSource` metadata marks provenance (`reassembled_chunks` or `file_read_fallback`).
   119	
   120	**Stage 4 — Filter + Annotate** (`stage4-filter.ts`):
   121	**Score immutability invariant**: Stage 4 MUST NOT modify scores. Enforced via compile-time `Stage4ReadonlyRow` readonly fields and runtime `captureScoreSnapshot` / `verifyScoreInvariant` defence-in-depth. Applies memory-state filtering, per-tier limits, evidence gap detection (Z-score confidence check), quality floor (`QUALITY_FLOOR=0.005`), and token budget truncation. Lowest-priority retained-history rows remain fallback evidence only when filters allow them.
   122	
   123	<!-- /ANCHOR:overview -->
   124	
   125	---
   126	
   127	## 2. KEY CONCEPTS
   128	<!-- ANCHOR:key-concepts -->
   129	
   130	### Reciprocal Rank Fusion (RRF)
   131	
   132	**Formula**: `score = Sum 1/(k + rank_i)` where k=40 (tuned for ~1000-memory corpus)
   133	
   134	**Why RRF?**
   135	- Parameter-free fusion (no weight tuning required)
   136	- Resilient to retrieval method failures (graceful degradation)
   137	- Citation: Cormack et al. "RRF outperforms Condorcet" (SIGIR 2009)
   138	
   139	**Enhancements (REQ-011):**
   140	- **10% Convergence Bonus**: Results in multiple sources get +10% score boost
   141	- **1.5x Graph Weight**: Graph-exclusive discoveries weighted higher for novelty
   142	- **Adaptive Fusion**: Intent-aware weighted RRF with opt-in evaluation mode (feature flag `SPECKIT_ADAPTIVE_FUSION`)
   143	- **MMR Diversity**: Maximal Marginal Relevance reranking reduces near-duplicate results
   144	- **Recency Boost**: Time-aware score adjustment favoring recently updated memories
   145	- **Co-activation Boost**: Graph-neighbor score propagation via 2-hop causal traversal
   146	
   147	**Example:**
   148	```javascript
   149	// Vector rank: 2, BM25 rank: 5, Graph rank: 1
   150	// RRF score = 1/(40+2) + 1/(40+5) + 1.5/(40+1)
   151	//           = 0.0238 + 0.0222 + 0.0366 = 0.0826
   152	// Convergence bonus: 0.0826 * 1.10 = 0.0909 (final)
   153	```
   154	
   155	### BM25 (Best Matching 25)
   156	
   157	**Formula**:
   158	```text
   159	score(D, Q) = Sum IDF(qi) * (tf(qi,D) * (k1+1)) / (tf(qi,D) + k1 * (1-b + b*|D|/avgdl))
   160	```
   161	
   162	**Parameters:**
   163	- `k1 = 1.2`: Term frequency saturation (higher = less saturation)
   164	- `b = 0.75`: Length normalization (0=ignore length, 1=full penalty)
   165	- `tf(qi,D)`: Term frequency of query term qi in document D
   166	- `|D|`: Document length, `avgdl`: Average document length
   167	- `IDF(qi)`: Inverse document frequency: `log((N - n(qi) + 0.5) / (n(qi) + 0.5) + 1)`
   168	
   169	**Why BM25?**
   170	- Handles term frequency saturation (repeated words don't dominate)
   171	- Length normalization (short docs not penalized unfairly)
   172	- Pure JavaScript implementation (REQ-028, no Python dependency)
   173	
   174	<a id="fts-capability-cascade-floor"></a>
   175	### FTS Capability Cascade Floor
   176	
   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:
   178	
   179	- `lexicalPath`: the lane that actually ran for lexical retrieval. Current packet-owned values are `fts5` and `unavailable`. The wider response schema also allows `like`, but packet `010` does not claim that lane for this runtime seam.
   180	- `fallbackState`: the truthful FTS capability outcome for the request.
   181	
   182	The forced-degrade matrix is:
   183	
   184	| `fallbackState` | Meaning | `lexicalPath` |
   185	|-----------------|---------|---------------|
   186	| `ok` | FTS5 compile probe passed, `memory_fts` exists, and BM25 ranking executed normally | `fts5` |
   187	| `compile_probe_miss` | `PRAGMA compile_options` does not report FTS5 support, so lexical work cannot run for this request | `unavailable` |
   188	| `missing_table` | FTS5 support is present, but `memory_fts` is missing at runtime | `unavailable` |
   189	| `no_such_module_fts5` | The SQLite engine rejects FTS5 usage with `no such module: fts5` | `unavailable` |
   190	| `bm25_runtime_failure` | The FTS5 table exists, but the `bm25(...)` ranking call fails at runtime | `unavailable` |
   191	
   192	The contract is intentionally narrow: preserve result-shape semantics, surface truthful lane metadata, and let later packets build on that truth instead of inferring capability from empty results or warning logs.
   193	
   194	### Intent-Aware Retrieval
   195	
   196	**7 Intent Types** (REQ-012, T036-T039):
   197	
   198	| Intent           | Description                  | Prioritizes                         |
   199	| ---------------- | ---------------------------- | ----------------------------------- |
   200	| `add_feature`    | Building new functionality   | Patterns, examples, architecture    |
   201	| `fix_bug`        | Debugging issues             | Error history, root cause, patches  |
   202	| `refactor`       | Restructuring code           | Patterns, dependencies, design docs |
   203	| `security_audit` | Security review              | Vulnerabilities, audit logs         |
   204	| `understand`     | Learning/exploring (default) | Explanations, context, decisions    |
   205	| `find_spec`      | Spec document retrieval      | Boosts spec-doc source weights      |
   206	| `find_decision`  | Decision rationale lookup    | Boosts decision-record source weights |
   207	
   208	**Detection**: Keyword matching with primary (2x weight) and secondary (1x weight) terms.
   209	
   210	**Example**:
   211	```javascript
   212	// Query: "add user registration feature"
   213	// Intent: add_feature
   214	// Boosts: architecture memories, pattern docs, examples
   215	```
   216	
   217	### Cross-Encoder Reranking
   218	
   219	**Purpose**: Refine top results using query-document pair scoring.
   220	

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
 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') {

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

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts | sed -n '1,260p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	// ───────────────────────────────────────────────────────────────
     2	// MODULE: Stage1 Candidate Gen
     3	// ───────────────────────────────────────────────────────────────
     4	// 4-stage retrieval pipeline architecture
     5	//
     6	// Responsibility: Execute search channels and collect raw candidate results.
     7	// This stage avoids downstream fusion/reranking, but may apply temporal
     8	// Contiguity to raw vector-channel hits before later pipeline stages.
     9	// Results are collected from the appropriate search channel based on search type.
    10	//
    11	// Search channels handled:
    12	//   - multi-concept: Generate per-concept embeddings, run multiConceptSearch
    13	//   - hybrid (deep mode): Query expansion + multi-variant hybrid search + dedup
    14	//   - hybrid (R12):       Embedding-based query expansion (SPECKIT_EMBEDDING_EXPANSION)
    15	// Suppressed when R15 classifies query as "simple" (mutual exclusion)
    16	//   - hybrid: collectRawCandidates → falls back to vector on failure
    17	//   - vector: Direct vectorSearch
    18	//
    19	// Post-channel operations:
    20	//   - Constitutional memory injection (if not already present)
    21	//   - Quality score filtering
    22	//   - Tier and contextType filtering
    23	//
    24	// I/O CONTRACT:
    25	// Input:  Stage1Input { config: PipelineConfig }
    26	// Output: Stage1Output { candidates: PipelineRow[], metadata }
    27	// Key invariants:
    28	//     - candidates contains raw channel scores; vector hits may include an
    29	//       optional temporal-contiguity boost applied before downstream fusion
    30	//     - Constitutional rows are always present when includeConstitutional=true and no tier filter
    31	//     - All rows pass qualityThreshold (if set) and tier/contextType filters
    32	// Side effects:
    33	//     - Generates query embeddings via the embeddings provider (external call)
    34	//     - Reads from the vector index and FTS5 / BM25 index (DB reads only)
    35	//
    36	import type { Stage1Input, Stage1Output, PipelineRow } from './types.js';
    37	import { resolveEffectiveScore } from './types.js';
    38	import * as vectorIndex from '../vector-index.js';
    39	import * as embeddings from '../../providers/embeddings.js';
    40	import * as hybridSearch from '../hybrid-search.js';
    41	import { vectorSearchWithContiguity } from '../../cognitive/temporal-contiguity.js';
    42	import { isMultiQueryEnabled, isEmbeddingExpansionEnabled, isMemorySummariesEnabled, isQueryDecompositionEnabled, isGraphConceptRoutingEnabled, isLlmReformulationEnabled, isHyDEEnabled, isQuerySurrogatesEnabled, isTemporalContiguityEnabled, isQueryConceptExpansionEnabled } from '../search-flags.js';
    43	import { expandQuery } from '../query-expander.js';
    44	import { expandQueryWithEmbeddings, isExpansionActive } from '../embedding-expansion.js';
    45	import { querySummaryEmbeddings, checkScaleGate } from '../memory-summaries.js';
    46	import { addTraceEntry } from '@spec-kit/shared/contracts/retrieval-trace';
    47	import { requireDb } from '../../../utils/db-helpers.js';
    48	import { filterRowsByScope } from '../../governance/scope-governance.js';
    49	import { withTimeout } from '../../errors/core.js';
    50	import { GRAPH_METADATA_MIGRATED_QUALITY_FLAG } from '../../graph/graph-metadata-schema.js';
    51	import { computeBackfillQualityScore } from '../../validation/save-quality-gate.js';
    52	import {
    53	  isMultiFacet,
    54	  decompose,
    55	  mergeByFacetCoverage as mergeFacetCoveragePools,
    56	  MAX_FACETS,
    57	} from '../query-decomposer.js';
    58	import { routeQueryConcepts, nounPhrases, getConceptExpansionTerms } from '../entity-linker.js';
    59	import { cheapSeedRetrieve, llm, fanout } from '../llm-reformulation.js';
    60	import { runHyDE } from '../hyde.js';
    61	import { matchSurrogates } from '../query-surrogates.js';
    62	import { loadSurrogatesBatch } from '../surrogate-storage.js';
    63	
    64	// Feature catalog: 4-stage pipeline architecture
    65	// Feature catalog: Hybrid search pipeline
    66	
    67	
    68	// -- Constants --
    69	
    70	/** Maximum number of deep-mode query variants to generate (original + expanded). */
    71	const MAX_DEEP_QUERY_VARIANTS = 3;
    72	
    73	/** F1: Deep-mode expansion timeout — fall back to base query if variants take too long. */
    74	const DEEP_EXPANSION_TIMEOUT_MS = 5000;
    75	
    76	/** Minimum cosine similarity for multi-concept search. */
    77	const MULTI_CONCEPT_MIN_SIMILARITY = 0.5;
    78	
    79	/** Number of constitutional results to fetch when none appear in hybrid/vector results. */
    80	const CONSTITUTIONAL_INJECT_LIMIT = 5;
    81	
    82	/** Number of similar memories to mine for R12 embedding-based query expansion terms. */
    83	const DEFAULT_EXPANSION_CANDIDATE_LIMIT = 5;
    84	
    85	/** D2: Timeout for facet decomposition parallel searches (ms). */
    86	const DECOMPOSITION_TIMEOUT_MS = 5000;
    87	const MAX_QUERY_DECOMPOSITION_FACETS = MAX_FACETS;
    88	
    89	// -- Helper Functions --
    90	
    91	/**
    92	 * Filter results by a minimum quality score threshold.
    93	 *
    94	 * - If no threshold is provided or it is not a finite number, all results pass.
    95	 * - Threshold is clamped to [0, 1].
    96	 * - Rows with a missing or non-finite `quality_score` are treated as 0.
    97	 *
    98	 * @param results - Candidate rows to filter.
    99	 * @param threshold - Minimum quality score in [0, 1] (inclusive).
   100	 * @returns Filtered array; original array returned unchanged when no threshold applies.
   101	 */
   102	function filterByMinQualityScore(
   103	  results: PipelineRow[],
   104	  threshold?: number
   105	): PipelineRow[] {
   106	  if (typeof threshold !== 'number' || !Number.isFinite(threshold)) {
   107	    return results;
   108	  }
   109	
   110	  const clampedThreshold = Math.max(0, Math.min(1, threshold));
   111	
   112	  return results.filter((row) => {
   113	    const rawScore = row.quality_score as number | undefined;
   114	    const score =
   115	      typeof rawScore === 'number' && Number.isFinite(rawScore) ? rawScore : 0;
   116	    return score >= clampedThreshold;
   117	  });
   118	}
   119	
   120	function backfillMissingQualityScores(results: PipelineRow[]): PipelineRow[] {
   121	  return results.map((row) => {
   122	    if (row.quality_score !== 0 && row.quality_score != null) {
   123	      return row;
   124	    }
   125	
   126	    return {
   127	      ...row,
   128	      quality_score: computeBackfillQualityScore(row),
   129	    };
   130	  });
   131	}
   132	
   133	function applyArchiveFilter(
   134	  results: PipelineRow[],
   135	  _includeArchived: boolean
   136	): PipelineRow[] {
   137	  return results;
   138	}
   139	
   140	function applyFolderFilter(
   141	  results: PipelineRow[],
   142	  specFolder?: string
   143	): PipelineRow[] {
   144	  if (!specFolder) return results;
   145	  return results.filter((row) => {
   146	    const rowSpecFolder = row.spec_folder ?? row.specFolder;
   147	    return rowSpecFolder === specFolder;
   148	  });
   149	}
   150	
   151	function applyTierFilter(
   152	  results: PipelineRow[],
   153	  tier?: string
   154	): PipelineRow[] {
   155	  if (!tier) return results;
   156	  return results.filter((row) => row.importance_tier === tier);
   157	}
   158	
   159	/**
   160	 * Resolve the effective context type from a pipeline row.
   161	 *
   162	 * Rows may carry context type under either `contextType` (camelCase) or
   163	 * `context_type` (snake_case). This function normalises the lookup.
   164	 *
   165	 * @param row - The pipeline row to inspect.
   166	 * @returns The context type string, or `undefined` if absent.
   167	 */
   168	function resolveRowContextType(row: PipelineRow): string | undefined {
   169	  if (typeof row.contextType === 'string' && row.contextType.length > 0) {
   170	    return row.contextType;
   171	  }
   172	  if (typeof row.context_type === 'string' && row.context_type.length > 0) {
   173	    return row.context_type;
   174	  }
   175	  return undefined;
   176	}
   177	
   178	function mergeStringLists(...values: unknown[]): string[] {
   179	  const merged = new Set<string>();
   180	  for (const value of values) {
   181	    if (!Array.isArray(value)) {
   182	      continue;
   183	    }
   184	    for (const entry of value) {
   185	      if (typeof entry === 'string' && entry.length > 0) {
   186	        merged.add(entry);
   187	      }
   188	    }
   189	  }
   190	  return Array.from(merged);
   191	}
   192	
   193	function readFiniteScoreMap(value: unknown): Record<string, number> {
   194	  if (!value || typeof value !== 'object' || Array.isArray(value)) {
   195	    return {};
   196	  }
   197	
   198	  const normalized: Record<string, number> = {};
   199	  for (const [key, score] of Object.entries(value as Record<string, unknown>)) {
   200	    if (typeof score === 'number' && Number.isFinite(score)) {
   201	      normalized[key] = score;
   202	    }
   203	  }
   204	  return normalized;
   205	}
   206	
   207	function readQualityFlags(value: unknown): string[] {
   208	  if (Array.isArray(value)) {
   209	    return value.filter((entry): entry is string => typeof entry === 'string' && entry.length > 0);
   210	  }
   211	  if (typeof value !== 'string' || value.trim().length === 0) {
   212	    return [];
   213	  }
   214	  try {
   215	    const parsed = JSON.parse(value) as unknown;
   216	    if (Array.isArray(parsed)) {
   217	      return parsed.filter((entry): entry is string => typeof entry === 'string' && entry.length > 0);
   218	    }
   219	  } catch {
   220	    // Fall back to comma-delimited parsing for legacy callers/tests.
   221	  }
   222	  return value
   223	    .split(',')
   224	    .map((entry) => entry.trim())
   225	    .filter((entry) => entry.length > 0);
   226	}
   227	
   228	function isMigratedGraphMetadataCandidate(row: PipelineRow): boolean {
   229	  const migratedValue = row.migrated ?? row.is_migrated ?? row.metadata_migrated;
   230	  if (migratedValue === true || migratedValue === 1 || migratedValue === '1' || migratedValue === 'true') {
   231	    return true;
   232	  }
   233	  const qualityFlags = readQualityFlags(row.quality_flags ?? row.qualityFlags);
   234	  return qualityFlags.includes(GRAPH_METADATA_MIGRATED_QUALITY_FLAG);
   235	}
   236	
   237	function mergeScoreMaps(...maps: Array<Record<string, number>>): Record<string, number> {
   238	  const merged: Record<string, number> = {};
   239	  for (const map of maps) {
   240	    for (const [key, score] of Object.entries(map)) {
   241	      if (!(key in merged) || score > merged[key]!) {
   242	        merged[key] = score;
   243	      }
   244	    }
   245	  }
   246	  return merged;
   247	}
   248	
   249	function getCandidateSources(row: PipelineRow): string[] {
   250	  const explicitSources = mergeStringLists(row.sources);
   251	  if (explicitSources.length > 0) {
   252	    return explicitSources;
   253	  }
   254	  return typeof row.source === 'string' && row.source.length > 0 ? [row.source] : [];
   255	}
   256	
   257	function getCandidateSourceScores(row: PipelineRow): Record<string, number> {
   258	  const sourceScores = readFiniteScoreMap(row.sourceScores);
   259	  if (Object.keys(sourceScores).length > 0) {
   260	    return sourceScores;

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts | sed -n '1,220p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	// ───────────────────────────────────────────────────────────────
     2	// MODULE: Stage2 Fusion
     3	// ───────────────────────────────────────────────────────────────
     4	// the rollout (R6): 4-Stage Retrieval Pipeline
     5	//
     6	// I/O CONTRACT:
     7	// Input:  Stage2Input { candidates: PipelineRow[], config, stage1Metadata }
     8	// Output: Stage2Output { scored: PipelineRow[], metadata }
     9	// Key invariants:
    10	//     - Every score modification in the pipeline happens exactly once here
    11	//     - Intent weights are NEVER applied to hybrid results (G2 double-weighting guard)
    12	//     - scored is sorted descending by effective composite score on exit
    13	// Side effects:
    14	//     - FSRS write-back to memory_index (when trackAccess=true) — DB write
    15	//     - Learned trigger and negative-feedback reads from DB
    16	//
    17	// PURPOSE: Single point for ALL scoring signals. Intent weights are
    18	// Applied ONCE here only — this is the architectural guard against
    19	// The G2 double-weighting recurrence bug.
    20	//
    21	// SIGNAL APPLICATION ORDER (must not be reordered — 13 steps):
    22	// 1.  Session boost           — working-memory attention amplification
    23	// 1a. Recency fusion          — time-decay bonus for recent memories
    24	// 2.  Causal boost            — graph-traversal neighbor amplification
    25	// 2a. Co-activation spreading — spreading activation from top-N seeds
    26	// 2b. Community co-retrieval  — N2c inject community co-members
    27	// 2c. Graph signals           — N2a momentum + N2b causal depth
    28	// 3.  Testing effect          — FSRS strengthening write-back (trackAccess)
    29	// 4.  Intent weights          — non-hybrid search post-scoring adjustment
    30	// 5.  Artifact routing        — class-based weight boosts
    31	// 6.  Feedback signals        — learned trigger boosts + negative demotions
    32	// 7.  Artifact limiting       — result count cap from routing strategy
    33	// 8.  Anchor metadata         — extract named ANCHOR sections (annotation)
    34	// 9.  Validation metadata     — spec quality signals enrichment + quality scoring
    35	//
    36	// Hybrid search already applies intent-aware scoring
    37	// Internally (RRF / RSF fusion). Post-search intent weighting is
    38	// Therefore ONLY applied for non-hybrid search types (vector,
    39	// Multi-concept). Applying it to hybrid results would double-count.
    40	//
    41	// SCORE AUDIT CONTRACT: Stage 2 writes the fused `score` field (steps 1-7).
    42	// Stage 3 (rerank) MAY overwrite `score` with the reranked value and MUST
    43	// preserve the original in `stage2Score` for auditability (see F2.02 fix).
    44	// Stage 4 (filter) MUST NOT mutate any score fields — it is read-only.
    45	// The canonical reranker output is `rerankerScore`; `score` is synced to it
    46	// for downstream consumer compatibility.
    47	
    48	import type Database from 'better-sqlite3';
    49	import path from 'path';
    50	import { readFile } from 'fs/promises';
    51	
    52	import { resolveEffectiveScore } from './types.js';
    53	import type { Stage2Input, Stage2Output, PipelineRow, IntentWeightsConfig, ArtifactRoutingConfig } from './types.js';
    54	
    55	import * as sessionBoost from '../session-boost.js';
    56	import * as causalBoost from '../causal-boost.js';
    57	import {
    58	  isEnabled as isCoActivationEnabled,
    59	  spreadActivation,
    60	  getRelatedMemoryCounts,
    61	  resolveCoActivationBoostFactor,
    62	} from '../../cognitive/co-activation.js';
    63	import type { SpreadResult } from '../../cognitive/co-activation.js';
    64	import { ensureAdaptiveTables, getAdaptiveMode } from '../../cognitive/adaptive-ranking.js';
    65	import * as fsrsScheduler from '../../cognitive/fsrs-scheduler.js';
    66	import { queryLearnedTriggers } from '../learned-feedback.js';
    67	import { applyNegativeFeedback, getNegativeFeedbackStats } from '../../scoring/negative-feedback.js';
    68	import {
    69	  isNegativeFeedbackEnabled,
    70	  isCommunityDetectionEnabled,
    71	  isGraphCalibrationProfileEnabled,
    72	  isGraphSignalsEnabled,
    73	  isUsageRankingEnabled,
    74	  resolveGraphWalkRolloutState,
    75	  isLearnedStage2CombinerEnabled,
    76	  isResultProvenanceEnabled,
    77	} from '../search-flags.js';
    78	import { applyGraphContributionCalibration } from '../graph-calibration.js';
    79	import { shadowScore, extractFeatureVector, loadModel } from '@spec-kit/shared/ranking/learned-combiner';
    80	import type { LearnedModel } from '@spec-kit/shared/ranking/learned-combiner';
    81	import { getAdaptiveWeights, isAdaptiveFusionEnabled } from '@spec-kit/shared/algorithms/adaptive-fusion';
    82	import { addTraceEntry } from '@spec-kit/shared/contracts/retrieval-trace';
    83	import { requireDb } from '../../../utils/db-helpers.js';
    84	import { computeRecencyScore } from '../../scoring/folder-scoring.js';
    85	import { enrichResultsWithAnchorMetadata } from '../anchor-metadata.js';
    86	import { enrichResultsWithValidationMetadata } from '../validation-metadata.js';
    87	// B4: Stage 2b enrichment extracted for decomposition clarity
    88	import { executeStage2bEnrichment } from './stage2b-enrichment.js';
    89	import { applyCommunityBoost } from '../../graph/community-detection.js';
    90	import { applyGraphSignals } from '../../graph/graph-signals.js';
    91	import { computeUsageBoost } from '../../graph/usage-ranking-signal.js';
    92	import { ensureUsageColumn } from '../../graph/usage-tracking.js';
    93	import { isGraphUnifiedEnabled } from '../graph-flags.js';
    94	import { resolveFusionIntentContract } from '../search-utils.js';
    95	import { sortDeterministicRows } from './ranking-contract.js';
    96	
    97	// Feature catalog: 4-stage pipeline architecture
    98	// Feature catalog: MPAB chunk-to-memory aggregation
    99	
   100	
   101	// -- Internal type aliases --
   102	
   103	/** A row with a resolved numeric base score for internal use. */
   104	interface ScoredRow extends PipelineRow {
   105	  intentAdjustedScore?: number;
   106	}
   107	
   108	/** Result of the strengthenOnAccess FSRS write-back. */
   109	interface StrengthenResult {
   110	  stability: number;
   111	  difficulty: number;
   112	}
   113	
   114	interface ValidationMetadataLike {
   115	  qualityScore?: number;
   116	  specLevel?: number;
   117	  completionStatus?: 'complete' | 'partial' | 'unknown';
   118	  hasChecklist?: boolean;
   119	}
   120	
   121	// -- Constants --
   122	
   123	/** Number of top results used as seeds for co-activation spreading. */
   124	const SPREAD_ACTIVATION_TOP_N = 5;
   125	const DEFAULT_LEARNED_STAGE2_MODEL_RELATIVE_PATH = path.join('models', 'learned-stage2-combiner.json');
   126	
   127	/** Recency fusion weight — controls how much recency score contributes to the fused score.
   128	 *  Env-tunable via SPECKIT_RECENCY_FUSION_WEIGHT (default 0.07). */
   129	const RECENCY_FUSION_WEIGHT = parseFloat(process.env.SPECKIT_RECENCY_FUSION_WEIGHT || '') || 0.07;
   130	
   131	/** Recency fusion cap — maximum bonus a candidate can receive from recency fusion.
   132	 *  Env-tunable via SPECKIT_RECENCY_FUSION_CAP (default 0.10). */
   133	const RECENCY_FUSION_CAP = parseFloat(process.env.SPECKIT_RECENCY_FUSION_CAP || '') || 0.10;
   134	
   135	const MIN_VALIDATION_MULTIPLIER = 0.8;
   136	const MAX_VALIDATION_MULTIPLIER = 1.2;
   137	
   138	type LearnedStage2ModelCacheEntry = {
   139	  path: string;
   140	  model: LearnedModel | null;
   141	};
   142	
   143	let cachedLearnedStage2Model: LearnedStage2ModelCacheEntry | null = null;
   144	let learnedStage2ModelLoadPromise: Promise<LearnedStage2ModelCacheEntry> | null = null;
   145	let learnedStage2ModelLoadPromisePath: string | null = null;
   146	
   147	function clampMultiplier(value: number): number {
   148	  if (!Number.isFinite(value)) return 1;
   149	  if (value < MIN_VALIDATION_MULTIPLIER) return MIN_VALIDATION_MULTIPLIER;
   150	  if (value > MAX_VALIDATION_MULTIPLIER) return MAX_VALIDATION_MULTIPLIER;
   151	  return value;
   152	}
   153	
   154	function isShadowLearningModelLoadEnabled(): boolean {
   155	  return process.env.SPECKIT_SHADOW_LEARNING?.toLowerCase().trim() === 'true';
   156	}
   157	
   158	function resolveLearnedStage2ModelPath(): string {
   159	  const configured = process.env.SPECKIT_LEARNED_STAGE2_MODEL?.trim();
   160	  if (!configured) {
   161	    return path.resolve(process.cwd(), DEFAULT_LEARNED_STAGE2_MODEL_RELATIVE_PATH);
   162	  }
   163	  if (path.isAbsolute(configured)) {
   164	    return configured;
   165	  }
   166	  return path.resolve(process.cwd(), configured);
   167	}
   168	
   169	async function loadPersistedLearnedStage2Model(): Promise<LearnedModel | null> {
   170	  if (!isShadowLearningModelLoadEnabled()) {
   171	    return null;
   172	  }
   173	
   174	  const modelPath = resolveLearnedStage2ModelPath();
   175	  if (cachedLearnedStage2Model?.path === modelPath) {
   176	    return cachedLearnedStage2Model.model;
   177	  }
   178	
   179	  if (learnedStage2ModelLoadPromise && learnedStage2ModelLoadPromisePath === modelPath) {
   180	    return (await learnedStage2ModelLoadPromise).model;
   181	  }
   182	
   183	  if (learnedStage2ModelLoadPromisePath !== modelPath) {
   184	    learnedStage2ModelLoadPromise = null;
   185	    learnedStage2ModelLoadPromisePath = null;
   186	  }
   187	
   188	  learnedStage2ModelLoadPromisePath = modelPath;
   189	  learnedStage2ModelLoadPromise = (async (): Promise<LearnedStage2ModelCacheEntry> => {
   190	    try {
   191	      const json = await readFile(modelPath, 'utf8');
   192	      const model = loadModel(json);
   193	      if (!model) {
   194	        console.warn(`[stage2-fusion] learned stage2 model at ${modelPath} is invalid; shadow scoring will use manual-only fallback`);
   195	      }
   196	      const entry = { path: modelPath, model };
   197	      cachedLearnedStage2Model = entry;
   198	      return entry;
   199	    } catch (err: unknown) {
   200	      const entry = { path: modelPath, model: null };
   201	      cachedLearnedStage2Model = entry;
   202	
   203	      const code = typeof err === 'object' && err !== null && 'code' in err
   204	        ? String((err as { code?: unknown }).code)
   205	        : '';
   206	      if (code !== 'ENOENT') {
   207	        const message = err instanceof Error ? err.message : String(err);
   208	        console.warn(`[stage2-fusion] learned stage2 model load failed: ${message}`);
   209	      }
   210	      return entry;
   211	    } finally {
   212	      learnedStage2ModelLoadPromise = null;
   213	      learnedStage2ModelLoadPromisePath = null;
   214	    }
   215	  })();
   216	
   217	  return (await learnedStage2ModelLoadPromise).model;
   218	}
   219	
   220	/**

exec
/bin/zsh -lc "nl -ba .opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/010-search-retrieval-quality-fixes/implementation-summary.md | sed -n '1,180p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
     1	---
     2	title: "Implementat [system-spec-kit/023-hybrid-rag-fusion-refinement/010-search-retrieval-quality-fixes/implementation-summary]"
     3	description: "Structured summary of the six retrieval quality fixes in memory context/search pipelines."
     4	trigger_phrases:
     5	  - "search retrieval implementation summary"
     6	  - "retrieval quality fixes summary"
     7	importance_tier: "important"
     8	contextType: "implementation"
     9	_memory:
    10	  continuity:
    11	    packet_pointer: "system-spec-kit/023-hybrid-rag-fusion-refinement/010-search-retrieval-quality-fixes"
    12	    last_updated_at: "2026-04-24T14:55:00Z"
    13	    last_updated_by: "copilot-gpt-5-4"
    14	    recent_action: "Backfilled memory block"
    15	    next_safe_action: "Revalidate packet docs"
    16	    key_files: ["implementation-summary.md"]
    17	template_source_hint: "<!-- SPECKIT_TEMPLATE_SOURCE: impl-summary-core | v2.2 -->"
    18	---
    19	<!-- SPECKIT_LEVEL: 2 -->
    20	<!-- SPECKIT_TEMPLATE_SOURCE: impl-summary-core | v2.2 -->
    21	
    22	# Implementation Summary
    23	<!-- HVR_REFERENCE: .opencode/skills/sk-doc/references/hvr_rules.md -->
    24	
    25	---
    26	
    27	<!-- ANCHOR:metadata -->
    28	## Metadata
    29	
    30	| Field | Value |
    31	|-------|-------|
    32	| **Spec Folder** | 010-search-retrieval-quality-fixes |
    33	| **Completed** | 2026-04-01 (implementation pass), 2026-04-02 (structural doc alignment) |
    34	| **Level** | 2 |
    35	<!-- /ANCHOR:metadata -->
    36	
    37	---
    38	
    39	<!-- ANCHOR:what-built -->
    40	## What Was Built
    41	
    42	This phase implemented six retrieval-quality fixes across context routing, folder discovery behavior, token budget handling, and intent classification. The changes targeted false zero-result outcomes and low-quality intent auto-detection paths.
    43	
    44	### Retrieval Quality Remediation
    45	
    46	The implementation updated strategy intent propagation, added recovery for over-narrow folder scope, introduced adaptive truncation behavior, wired folder boost scoring metadata, added two-tier metadata/content response behavior, and added a confidence floor that defaults weak auto-detections to `understand`.
    47	
    48	### Files Changed
    49	
    50	| File | Action | Purpose |
    51	|------|--------|---------|
    52	| `mcp_server/handlers/memory-context.ts` | Modified | Intent propagation, folder recovery, adaptive truncation, two-tier behavior |
    53	| `mcp_server/handlers/memory-search.ts` | Modified | Folder boost application + intent confidence floor |
    54	| `mcp_server/lib/search/folder-discovery.ts` | Modified | Folder discovery support for scoring signal integration |
    55	<!-- /ANCHOR:what-built -->
    56	
    57	---
    58	
    59	<!-- ANCHOR:how-delivered -->
    60	## How It Was Delivered
    61	
    62	Implementation was performed in staged fixes with incremental verification. Structural documentation in this phase was realigned on 2026-04-02 to match required template anchors and headers so strict recursive validation can pass without format errors.
    63	<!-- /ANCHOR:how-delivered -->
    64	
    65	---
    66	
    67	<!-- ANCHOR:decisions -->
    68	## Key Decisions
    69	
    70	| Decision | Why |
    71	|----------|-----|
    72	| Keep recovery logic for narrow folder scope while introducing folder boost signal | Preserves safe fallback behavior for known 0-result edge case |
    73	| Apply confidence floor only to auto-detected intents | Explicit caller intent should not be overridden |
    74	| Separate structural doc remediation from runtime verification claims | Prevents overstating confidence when cache-sensitive runtime checks are pending |
    75	<!-- /ANCHOR:decisions -->
    76	
    77	---
    78	
    79	<!-- ANCHOR:verification -->
    80	## Verification
    81	
    82	| Check | Result |
    83	|-------|--------|
    84	| Phase docs now use required template section headers | PASS |
    85	| Required anchor pairs in this file present | PASS |
    86	| Runtime retrieval checks (fresh restart/cache state) | PENDING |
    87	| Recursive strict validator rerun after full phase patchset | PENDING |
    88	<!-- /ANCHOR:verification -->
    89	
    90	---
    91	
    92	<!-- ANCHOR:limitations -->
    93	## Known Limitations
    94	
    95	1. Runtime confirmation for all retrieval scenarios is pending a fresh server/cache verification pass.
    96	2. This summary intentionally avoids introducing new completion claims beyond documented implementation scope.
    97	<!-- /ANCHOR:limitations -->

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     1	---
     2	title: "Implementati [system-spec-kit/023-hybrid-rag-fusion-refinement/013-fts5-fix-and-search-dashboard/implementation-summary]"
     3	description: "Post-implementation summary — to be completed after Items 3 and 4 are implemented."
     4	trigger_phrases:
     5	  - "fts5 fix implementation summary"
     6	  - "db path drift implementation summary"
     7	  - "search dashboard implementation summary"
     8	importance_tier: "normal"
     9	contextType: "implementation"
    10	_memory:
    11	  continuity:
    12	    packet_pointer: "system-spec-kit/023-hybrid-rag-fusion-refinement/013-fts5-fix-and-search-dashboard"
    13	    last_updated_at: "2026-04-24T14:55:00Z"
    14	    last_updated_by: "copilot-gpt-5-4"
    15	    recent_action: "Backfilled memory block"
    16	    next_safe_action: "Revalidate packet docs"
    17	    key_files: ["implementation-summary.md"]
    18	template_source_hint: "<!-- SPECKIT_TEMPLATE_SOURCE: level_2/implementation-summary.md | v2.2 -->"
    19	---
    20	<!-- SPECKIT_LEVEL: 2 -->
    21	<!-- SPECKIT_TEMPLATE_SOURCE: level_2/implementation-summary.md | v2.2 -->
    22	
    23	# Implementation Summary: FTS5 Fix, Search Dashboard, and DB Path Drift Fix
    24	<!-- HVR_REFERENCE: .opencode/skills/sk-doc/references/hvr_rules.md -->
    25	
    26	---
    27	
    28	<!-- ANCHOR:metadata -->
    29	## Metadata
    30	
    31	| Field | Value |
    32	|-------|-------|
    33	| **Spec Folder** | 013-fts5-fix-and-search-dashboard |
    34	| **Completed** | 2026-04-01 — All 4 items implemented and verified |
    35	| **Level** | 2 |
    36	<!-- /ANCHOR:metadata -->
    37	
    38	---
    39	
    40	<!-- ANCHOR:what-built -->
    41	## What Was Built
    42	
    43	All 4 items implemented, compiled, and verified at runtime.
    44	
    45	### Item 1 — FTS5 Double-Quoting Fix
    46	
    47	Multi-word searches now return FTS5-backed results. A guard at `sqlite-fts.ts` line 58 prevents tokens already wrapped in double quotes from being re-quoted, eliminating the invalid `""phrase""` syntax that caused SQLite to silently drop all FTS5 results for multi-word queries.
    48	
    49	### Item 2 — Search Dashboard Redesign
    50	
    51	The `/memory:search` output groups results by spec folder using leaf folder names (Design 10: folder-as-tree-group). Paths are no longer rendered at full length, making results scannable. Applied to both `.opencode/commands/memory/search.md` and `.agents/commands/memory/search.toml`.
    52	
    53	### Item 3 — DB Path Drift Fix (4-layer defense-in-depth)
    54	
    55	Root cause: `resolve_database_path()` in `vector-index-store.ts` drifted to empty provider-specific databases after Voyage-4 lazy initialization. Four independent fixes applied:
    56	
    57	1. **Path stabilization** (`vector-index-store.ts` lines 277-289): `resolve_database_path()` validates against drift — detects and logs when provider would derive a different path than the one already in use.
    58	2. **Empty DB rebind guard** (`db-state.ts` lines 294-310): `reinitializeDatabase()` refuses to rebind consumers to an empty database (0 memories). Override available via `SPECKIT_FORCE_REBIND=true`.
    59	3. **Startup health check** (`context-server.ts` lines 1368-1374): Database path logged on startup; initialization sequence confirms DB is populated before consumers activate.
    60	4. **Connection caching** (`vector-index-store.ts` lines 763-771): Connections cached post-validation only, preventing stale references to drifted paths.
    61	
    62	### Item 4 — Silent Failure Remediation
    63	
    64	31+ warning logs added across 5 search pipeline files. Every `return []` or `return null` on unexpected conditions now logs a `console.warn` with `[module-name]` prefix before returning. Affected files: `hybrid-search.ts` (8+), `stage1-candidate-gen.ts` (11+), `vector-index-queries.ts` (12+). FTS scope filter updated to match exact-or-descendant folders via `LIKE ? || "/%"` pattern at `sqlite-fts.ts` lines 63-65.
    65	
    66	### Files Changed
    67	
    68	| File | Action | Purpose |
    69	|------|--------|---------|
    70	| `mcp_server/lib/search/sqlite-fts.ts` | Modified | FTS5 double-quote guard + descendant scope filter |
    71	| `mcp_server/lib/search/vector-index-store.ts` | Modified | Stable `resolve_database_path()`, connection caching |
    72	| `mcp_server/core/db-state.ts` | Modified | Empty DB rebind guard in `reinitializeDatabase()` |
    73	| `mcp_server/context-server.ts` | Modified | Startup health check + DB path logging |
    74	| `mcp_server/lib/search/hybrid-search.ts` | Modified | 8+ warning logs on silent failure paths |
    75	| `mcp_server/lib/search/pipeline/stage1-candidate-gen.ts` | Modified | 11+ warning logs on failure paths |
    76	| `mcp_server/lib/search/vector-index-queries.ts` | Modified | 12+ warning logs on failure paths |
    77	| `.opencode/commands/memory/search.md` | Modified | Design 10 dashboard applied |
    78	| `.agents/commands/memory/search.toml` | Modified | Design 10 dashboard applied |
    79	| `mcp_server/handlers/memory-context.ts` | Modified | P0: folder discovery no longer promotes to specFolder filter |
    80	| `mcp_server/lib/search/pipeline/stage1-candidate-gen.ts` | Modified | P0: sessionId removed from governance scope check; P1: activeChannels metric |
    81	| `mcp_server/lib/search/pipeline/types.ts` | Modified | P1: `activeChannels` optional field in Stage1Output |
    82	| `mcp_server/lib/search/pipeline/stage2-fusion.ts` | Modified | P2: graph zero-contribution diagnostic warning |
    83	<!-- /ANCHOR:what-built -->
    84	
    85	---
    86	
    87	<!-- ANCHOR:how-delivered -->
    88	## How It Was Delivered
    89	
    90	All fixes applied directly to TypeScript source, compiled with `bun run build` (1210+ dist files), and verified at runtime. `memory_search("semantic search")` confirmed returning 5 results via hybrid pipeline (vector + keyword channels, cross-encoder reranking) in 812ms. Root cause investigation: 10 deep-research iterations + 10 deep-review iterations via Copilot CLI GPT 5.4 (documented in `scratch/`).
    91	<!-- /ANCHOR:how-delivered -->
    92	
    93	---
    94	
    95	<!-- ANCHOR:decisions -->
    96	## Key Decisions
    97	
    98	| Decision | Why |
    99	|----------|-----|
   100	| Guard pre-quoted tokens in `sqlite-fts.ts` rather than changing `bm25-index.ts` | The quoting in `bm25-index.ts` is intentional for the BM25 pipeline; the bug is in re-quoting at the FTS5 output stage only |
   101	| Design 10 (folder-as-tree-group) selected for dashboard | Balances readability and information density; leaf folder names are unique enough for identification without full paths |
   102	| Fail-closed on missing `MEMORY_DB_PATH` (Item 3, pending) | Silent fallback to a derived path is the source of the drift bug; fail-closed prevents the same class of error recurring |
   103	<!-- /ANCHOR:decisions -->
   104	
   105	---
   106	
   107	<!-- ANCHOR:verification -->
   108	## Verification
   109	
   110	| Check | Result |
   111	|-------|--------|
   112	| FTS5 guard present in sqlite-fts.ts line 58 | PASS |
   113	| `bun run build` after FTS5 fix | PASS — exit 0 |
   114	| Design 10 applied to search.md | PASS |
   115	| Design 10 applied to search.toml | PASS |
   116	| DB path drift fix — resolve_database_path() stabilized | PASS — lines 277-289 validated |
   117	| Empty DB rebind guard in reinitializeDatabase() | PASS — lines 294-310, refuses empty rebind |
   118	| Startup health check + DB path log | PASS — context-server.ts lines 1368-1374 |
   119	| Silent failure remediation (31+ warnings) | PASS — hybrid-search, stage1, vector-index-queries |
   120	| Runtime: memory_search returns results | PASS — 5 results, 812ms, hybrid pipeline |
   121	| P0: memory_context focused mode returns results | PASS — 5 candidates found (was 0); folder discovery no longer filters |
   122	| P0: sessionId not in governance scope check | PASS — 8 candidates in deep mode; no scope filtering despite ephemeral sessionId |
   123	| P1: activeChannels in stage1 metadata | PASS — `activeChannels: 2` in hybrid mode |
   124	| P2: graph zero-contribution diagnostic | PASS — all graphContribution fields 0 with rolloutState visible |
   125	<!-- /ANCHOR:verification -->
   126	
   127	---
   128	
   129	<!-- ANCHOR:limitations -->
   130	## Known Limitations
   131	
   132	1. **SPECKIT_FORCE_REBIND bypass**: The empty DB rebind guard can be overridden with `SPECKIT_FORCE_REBIND=true`. This is intentional for edge cases where provider-specific DBs are deliberately used, but could mask legitimate drift if set permanently.
   133	2. **Warning log volume**: 31+ new warning logs fire only on actual failure paths, not normal operation. If a deployment has persistent misconfiguration, logs may be noisy until the root cause is fixed.
   134	<!-- /ANCHOR:limitations -->
   135	
   136	---
   137	
   138	<!--
   139	CORE TEMPLATE: Post-implementation documentation, created AFTER work completes.
   140	Write in human voice: active, direct, specific. No em dashes, no hedging, no AI filler.
   141	HVR rules: .opencode/skills/sk-doc/references/hvr_rules.md
   142	-->

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   336	The Memory Engine is a local-first cognitive memory system built as an MCP server. `generate-context.js` updates canonical packet continuity and may emit supporting generated context artifacts inside the spec folder. Canonical continuity lives in the spec packet itself: use `/spec_kit:resume` as the recovery surface, then rebuild context in this order: `handover.md` -> `_memory.continuity` -> canonical spec docs. The MCP server indexes those packet-local sources with vector embeddings, BM25 and FTS5 full-text search, and `memory_match_triggers()` can still surface relevant prior context automatically when deeper retrieval is needed.
   337	
   338	`/memory:save` refreshes packet metadata on every invocation, and `session_resume` binds `args.sessionId` to transport caller context by default; set `MCP_SESSION_RESUME_AUTH_MODE=permissive` for rollout canaries. Copilot, Claude, and Gemini all share the same compact-cache provenance path.
   339	
   340	The memory engine includes a compact code graph and session lifecycle surfaces alongside hybrid retrieval.
   341	
   342	The full MCP API reference is in the [MCP Server README](.opencode/skills/system-spec-kit/mcp_server/README.md).
   343	
   344	&nbsp;
   345	#### Layered MCP Surface
   346	
   347	The MCP tools are organized into a layered architecture. Each layer has a token budget that controls how much context it consumes:
   348	
   349	| Layer | Name | Tools | Token Budget | Purpose |
   350	|-------|------|-------|-------------|---------|
   351	| **L1** | Orchestration | 3 | 2,000 | Unified context, resume, and bootstrap entry points |
   352	| **L2** | Core | 4 | 1,500 | Search, quick search, trigger matching, save |
   353	| **L3** | Discovery | 4 | 800 | List, stats, health checks, and session readiness |
   354	| **L4** | Mutation | 4 | 500 | Delete, update, validate, bulk cleanup |
   355	| **L5** | Lifecycle | 4 | 600 | Checkpoints and lifecycle state |
   356	| **L6** | Analysis | 10 | 1,200 | Causal graph, epistemic baselines, evaluations, and dashboards |
   357	| **L7** | Maintenance | 10 | 1,000 | Index scans, async ingest, learning history, and graph/CocoIndex maintenance |
   358	| | **Total** | **47** | **8,400** | |
   359	
   360	Lower layers load only when needed. L1 is always available. L2 loads for any search. L3-L7 load based on the specific command being used.
   361	
   362	&nbsp;
   363	#### Hybrid Search
   364	
   365	Every search checks five core channels at once, with CocoIndex available as a semantic code search bridge:
   366	
   367	- **Vector** - Semantic similarity via embeddings. Finds related content when words differ.
   368	- **FTS5** - Full-text search on exact words and phrases.
   369	- **BM25** - Keyword relevance scoring.
   370	- **Causal Graph** - Follows cause-and-effect links between memories.
   371	- **Degree** - Scores by graph connectivity, weighted by edge type.
   372	
   373	**Reciprocal Rank Fusion (RRF)** combines results across channels so memories scoring well in multiple channels rise to the top. **Graph-first routing** dispatches structural queries to the Code Graph first, then CocoIndex for semantic code discovery, then the memory pipeline. A **3-tier FTS fallback** activates when graph and semantic channels miss: FTS5 full-text, BM25 keyword scoring, then Grep/Glob filesystem search. The system truncates weak results and ensures every active channel is represented.
   374	
   375	&nbsp;
   376	#### Search Pipeline
   377	
   378	Every search passes through 4 stages:
   379	
   380	- **Candidate generation** - Parallel retrieval from the active channels plus constitutional injection where applicable.
   381	- **Fusion** - RRF-based scoring with post-fusion signals such as co-activation, FSRS decay, interference control, intent weights, and graph/session boosts when enabled.
   382	- **Rerank** - Cross-encoder reranking with chunk reassembly, a minimum Stage 3 gate of 4 candidates, and compatibility-only length-penalty wiring that resolves to a neutral `1.0` multiplier. `getRerankerStatus()` exposes latency plus cache hits, misses, stale hits, and evictions; if the reranker is unavailable, Stage 2 order is preserved with degraded metadata.
   383	- **Filtering** - State/quality filtering, confidence annotation, token-budget enforcement, and final response shaping without mutating post-rerank scores.
   384	
   385	&nbsp;
   386	#### Query Intelligence
   508	### 🔍 CocoIndex + Code Graph
   509	
   510	The framework uses two different code-understanding systems on purpose. **CocoIndex** handles semantic discovery, so the assistant can answer "find code that does X" or "how is Y implemented?" without knowing exact symbols first. The **Code Graph** handles structural expansion, so the assistant can answer questions like "what calls this?", "what imports this?", or "what breaks if we change it?" using an indexed relationship graph.
   511	
   512	The intended routing order is graph-first: the code graph resolves structural queries first, CocoIndex finds semantic candidates when structural resolution misses, and Memory supports session decisions and active-task context after the packet-local recovery sources have been checked. A 3-tier FTS fallback escalates automatically when results are weak.
   513	
   514	&nbsp;
   515	#### How the Code Graph Works
   516	
   517	The Code Graph is a SQLite-backed structural index that ships as part of the Spec Kit MCP server (`context-server.ts`). It is available to **every supported CLI** - Claude Code, Codex CLI, Gemini CLI, and GitHub Copilot - because each runtime connects to the same MCP server via its own config (`.claude/mcp.json`, `.mcp.json`, `.codex/config.toml`, `.agents/mcp.json`).
   518	
   519	**Startup injection.** When the MCP server starts, it initializes the `code-graph.sqlite` database, runs a non-blocking startup scan, and activates a file watcher. All four supported runtimes (Claude Code, Gemini CLI, GitHub Copilot, Codex CLI) transport the same compact startup shared-payload through their runtime hooks (`session-prime.ts` on Claude/Gemini/Copilot, `session-start.ts` on Codex). The payload includes a one-line health summary, `graphQualitySummary` (detector provenance + edge-enrichment summary), and the `sharedPayloadTransport` envelope so downstream consumers receive identical structural context regardless of runtime. `session_bootstrap()` remains available as a manual recovery surface when native hooks are disabled.
   520	
   521	**Auto-indexing.** The graph stays current through three mechanisms:
   522	1. **Startup scan** - indexes on server boot (async, non-blocking)
   523	2. **File watcher** - Chokidar monitors spec and source folders with a 2-second debounce, reindexing changed files in real time
   524	3. **Lazy refresh** - `code_graph_query` calls `ensureCodeGraphReady()` which detects staleness and triggers a bounded inline refresh before returning results
   525	
   526	The indexer uses tree-sitter to parse source files and extract functions, classes, imports, and call relationships. It tracks per-file content hashes to skip unchanged files, making incremental scans fast.
   527	
   528	&nbsp;
   529	#### Readiness & Response Contract
   530	
   531	`code_graph_query` and `code_graph_context` share a readiness-aware response contract. When the graph is fresh enough, both return `status: "ok"` with resolved results plus a `readiness` / `canonicalReadiness` / `trustState` block. When readiness requires a full scan that cannot run inline, both return an explicit **`status: "blocked"`** payload naming `requiredAction: "code_graph_scan"`, `blockReason: "full_scan_required"`, `degraded`, and `graphAnswersOmitted` instead of silently returning empty results. Callers should run `code_graph_scan` before retrying.
   532	
   533	Success payloads of `code_graph_context` carry structured `data.metadata.partialOutput` (`isPartial`, `reasons`, `omittedSections`, `omittedAnchors`, `truncatedText`) and an explicit `deadlineMs` field so callers can distinguish a complete answer from one trimmed by deadline or budget pressure. `code_graph_status` exposes `graphQualitySummary` (detector provenance + edge-enrichment confidence). CALLS queries on ambiguous subjects (e.g. `handle*`) prefer callable implementation nodes over wrapper-shadow candidates, and return ambiguity / selected-candidate metadata so callers can audit the choice.
   534	
   535	&nbsp;
   536	#### Edge Explanations and Better Blast Radius
   537	
   538	Relationship answers from `code_graph_query` include short `reason` and `step` fields alongside confidence and provenance, so you can see *why* an edge is there instead of just *that* it exists. `code_graph_context` carries those same fields through to structured edges and text briefs.
   539	
   540	`blast_radius` keeps the prior payload (affected files, source files, hot files, multi-file union, depth) and adds:
   541	
   542	- **`depthGroups`** — affected nodes bucketed by how far they sit from the change
   543	- **`riskLevel`** — `high` when the subject is ambiguous or fans out to more than 10 things at depth one, `medium` for 4–10, `low` otherwise
   544	- **`minConfidence`** filter — drop traversals below a confidence floor
   545	- **`ambiguityCandidates`** — list of plausible matches when the subject can't be resolved
   546	- **`failureFallback`** — structured info instead of a bare error string when resolution can't continue
   547	
   548	All of this rides inside the existing `code_edges.metadata` JSON blob — no SQLite schema changes.
   549	
   550	&nbsp;
   551	#### `detect_changes` — Preflight Impact Check
   552	
   553	`detect_changes` is a read-only Code Graph tool that takes a diff and tells you which symbols and files it touches. It runs alongside `code_graph_scan`, `code_graph_query`, `code_graph_status`, and `code_graph_context`.
   554	
   555	You hand it `{ diff: string, rootDir?: string }`. It walks each diff hunk, overlaps the line ranges with stored symbols, and returns `{ status, affectedSymbols[], affectedFiles[], blockedReason?, timestamp, readiness }`.
   556	
   557	Safety is non-negotiable: the tool checks the graph is fresh before parsing the diff. If the graph is stale or unavailable, it returns `status: 'blocked'` immediately — you never get a false "nothing impacted" answer from an out-of-date index. Inline indexing is explicitly disabled here, so the read-only contract is enforced.
   558	
   559	Under the hood the scan runner is split into four declared phases (`find-candidates` → `parse-candidates` → `finalize` → `emit-metrics`) for clearer instrumentation, with no SQLite schema changes.
   560	
   561	&nbsp;
   562	#### What Each System Does
   563	
   564	| System | Best for | Primary surface |
   565	|-------|----------|-----------------|
   566	| **CocoIndex** | Concept search, similar implementations, unfamiliar modules | `mcp__cocoindex_code__search` |
   567	| **Code Graph** | Callers, imports, symbol outlines, impact analysis, neighborhood expansion | `code_graph_scan`, `code_graph_query`, `code_graph_status`, `code_graph_context` |
   568	| **Session bridge tools** | Session bootstrap, resume, and health checks around graph availability | `session_bootstrap`, `session_resume`, `session_health` |
   569	| **CCC utilities** | CocoIndex availability, reindexing, result feedback | `ccc_status`, `ccc_reindex`, `ccc_feedback` |
   570	
   571	&nbsp;
   572	#### How Query Routing Works (Graph-First)
   573	
   574	The default routing order is: **Code Graph** (structural) -> **CocoIndex** (semantic code) -> **Memory** (session/decision context). This graph-first approach tries structural resolution before semantic similarity, with a 3-tier FTS fallback when earlier stages miss.
   575	
   576	- Use the **Code Graph** first for structural questions: callers, callees, imports, hierarchy, file outlines, and reverse impact.
   577	- Use **CocoIndex** for semantic and intent-based questions: "find code that validates memory quality", "show similar routing patterns", "where is the logic for X?"
   578	- Use **session tools** when recovering or checking environment readiness, but treat `/spec_kit:resume` as the canonical operator-facing recovery surface.
   579	- Rebuild task continuity in this order: `handover.md` -> `_memory.continuity` -> canonical spec docs.
   580	- Use **Memory** after those packet-local sources when the question is about prior decisions, spec history, handovers, or task continuity that still needs deeper retrieval.
   581	
   582	&nbsp;
   583	#### Why It Matters
   584	
   585	This split avoids forcing one search system to do everything poorly. Semantic search is good at resemblance. Structural search is good at relationships. Keeping both lets the framework move from "this code looks relevant" to "this is how it connects" without collapsing those concerns into a single noisy result set.
   586	

exec
/bin/zsh -lc "nl -ba .opencode/skills/system-spec-kit/SKILL.md | sed -n '566,607p'; nl -ba .opencode/skills/system-spec-kit/SKILL.md | sed -n '775,801p'" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
   566	Context preservation across sessions via 5-channel hybrid retrieval (vector, FTS5, BM25, graph, and degree) with Reciprocal Rank Fusion, intent-aware routing, and post-fusion reranking/filtering.
   567	
   568	**Server:** `@spec-kit/mcp-server` v1.7.2 - `context-server.ts` with 51 MCP tools across 7 layers. The tool surface is defined in `mcp_server/tool-schemas.ts`.
   569	
   570	**Memory Commands:** 4 memory slash commands (`/memory:save`, `/memory:manage`, `/memory:learn`, `/memory:search`) cover the spec-doc record command surface, while `/spec_kit:resume` owns session recovery through the broader memory/session recovery stack. The `spec_kit` surface now uses `/spec_kit:plan --intake-only` as the standalone intake workflow; `/spec_kit:plan` and `/spec_kit:complete` execute the shared intake contract (`.opencode/skills/system-spec-kit/references/intake-contract.md`) inline when the Step 0 local `folder_state` shows repair or creation is needed, and downstream callers should consume the contract's canonical `start_state` rather than reusing the local classifier name. `/spec_kit:deep-research` follows `../sk-deep-research/references/spec_check_protocol.md` for bounded `spec.md` anchoring. The `/memory:search` command covers all analysis and retrieval workflows. See `.opencode/commands/memory/`, `.opencode/commands/spec_kit/plan.md`, `.opencode/commands/spec_kit/complete.md`, `.opencode/skills/system-spec-kit/references/intake-contract.md`, and `.opencode/commands/spec_kit/resume.md` for command documentation.
   571	
   572	**MCP Tools (18 most-used of 47 total - see [memory_system.md](./references/memory/memory_system.md) for full reference):**
   573	
   574	| Tool                            | Layer | Purpose                                           |
   575	| ------------------------------- | ----- | ------------------------------------------------- |
   576	| `memory_context()`              | L1    | Unified entry point - modes: auto, quick, deep, focused, resume |
   577	| `memory_search()`               | L2    | 5-channel hybrid retrieval with intent-aware routing, channel normalization, graph/degree signals, reranking, and filtered output |
   578	| `memory_quick_search()`         | L2    | Simplified search (query + optional spec folder)  |
   579	| `memory_match_triggers()`       | L2    | Trigger matching + cognitive (decay, tiers, co-activation) |
   580	| `memory_save()`                 | L2    | Index a saved continuity artifact or spec doc with pre-flight validation |
   581	| `memory_list()`                 | L3    | Browse stored spec-doc records with pagination (parent rows by default) |
   582	| `memory_delete()`               | L4    | Delete memories by ID or spec folder              |
   583	| `checkpoint_create()`           | L5    | Create gzip-compressed checkpoint snapshot        |
   584	| `checkpoint_restore()`          | L5    | Transaction-wrapped restore with rollback         |
   585	| `memory_stats()`                | L3    | System statistics and memory counts                |
   586	| `memory_health()`              | L3    | Diagnostics: orphan detection, index consistency   |
   587	| `memory_index_scan()`          | L7    | Workspace scanning and re-indexing                 |
   588	| `checkpoint_list()`            | L5    | List available checkpoint snapshots                |
   589	| `checkpoint_delete()`          | L5    | Delete checkpoint by name (with confirmName safety)|
   590	
   591	> **Search architecture:** The search pipeline uses a 4-stage architecture (candidate generation → fusion → reranking → filtering). Current retrieval uses five channels, normalizes fallback thresholds correctly, keeps disabled channels disabled through fallback, defers irreversible confidence truncation until after reranking, and enforces token budgets using actual post-truncation counts. Adaptive fusion includes an internal continuity profile (`semantic 0.52`, `keyword 0.18`, `recency 0.07`, `graph 0.23`), Stage 3 uses a minimum rerank gate of 4 candidates, the retained `applyLengthPenalty` input is a compatibility no-op, and `getRerankerStatus()` exposes reranker cache hits, misses, stale hits, and evictions. See [search/README.md](./mcp_server/lib/search/README.md) for pipeline details, scoring algorithms, and graph signal features.
   592	
   593	**memory_context() - Mode Routing:**
   594	
   595	| Mode | Token Budget | When `mode=auto`: Intent Routing |
   596	| --- | --- | --- |
   597	| `quick` | 800 | - |
   598	| `deep` | 3500 | `add_feature`, `refactor`, `security_audit` |
   599	| `focused` | 3000 | `fix_bug`, `understand` |
   600	| `resume` | 1200 | - |
   601	
   602	**memory_search() - Key Rules:**
   603	- **REQUIRED:** `query` (string) OR `concepts` (2-5 strings). `specFolder` alone causes E040 error.
   604	- Use `anchors` with `includeContent: true` for token-efficient section retrieval (~90% savings).
   605	- Intent weights auto-adjust scoring: `fix_bug` boosts recency, `security_audit` boosts importance, `refactor`/`understand` boost similarity.
   606	- **Full parameter reference:** See [memory_system.md](./references/memory/memory_system.md)
   607	
   775	**Architecture:** CocoIndex (semantic, external MCP) finds code by concept. Code Graph (structural, this system) maps imports, calls, hierarchy. Memory (session, existing MCP) preserves decisions. The compact-merger combines all three under a 4000-token budget for compaction injection.
   776	
   777	**Budget allocator floors:** constitutional 700, codeGraph 1200, cocoIndex 900, triggered 400, overflow pool 800.
   778	
   779	**Source:** `mcp_server/code_graph/lib/` | `mcp_server/code_graph/handlers/`
   780	
   781	**Parser:** Tree-sitter WASM is the default structural parser for JS/TS/Python/Shell. Set `SPECKIT_PARSER=regex` for regex fallback. Parser adapter pattern allows future language additions.
   782	
   783	**Edge types:** CONTAINS, CALLS, IMPORTS, EXPORTS, EXTENDS, IMPLEMENTS, DECORATES, OVERRIDES, TYPE_OF.
   784	
   785	**Read-path freshness:** Startup and bootstrap surfaces report graph freshness without mutating the index. Bounded inline refresh happens on structural read paths when stale sets are small; otherwise callers receive `readiness` guidance to run `code_graph_scan`.
   786	
   787	**Blocked/degraded contract:** when readiness requires a suppressed `full_scan`, both `code_graph_query` and `code_graph_context` return an explicit `status: "blocked"` payload with `requiredAction: "code_graph_scan"`, `blockReason: "full_scan_required"`, `degraded`, and `graphAnswersOmitted` instead of silently returning empty results. This is uniform across query and context reads.
   788	
   789	**Context metadata:** `code_graph_context` success payloads carry structured `data.metadata.partialOutput` (`isPartial`, `reasons`, `omittedSections`, `omittedAnchors`, `truncatedText`) plus an explicit `deadlineMs` field so callers can distinguish a complete answer from one trimmed by deadline or budget pressure. `code_graph_status` exposes `graphQualitySummary` (detector provenance + edge-enrichment confidence). CocoIndex seed fidelity preserves `score`, `snippet`, and range metadata through context resolution.
   790	
   791	**CALLS disambiguation:** `code_graph_query` CALLS mode on ambiguous subjects (e.g. `handle*`) prefers callable implementation nodes over wrapper-shadow candidates, and records ambiguity / selected-candidate metadata so callers can audit the choice.
   792	
   793	**Startup payload parity:** all four runtimes (Claude, Gemini, Copilot, Codex) transport the same compact startup shared-payload through their runtime-specific startup hooks, including the `graphQualitySummary` summary. `session_bootstrap()` remains available as a manual recovery surface when native hooks are disabled.
   794	
   795	`lib/code-graph/readiness-contract.ts` is now the shared readiness source for query, scan, status, context, and CCC handlers. Its readiness blocks project onto the canonical `SharedPayloadTrustState` type instead of introducing a new local trust-state enum.
   796	
   797	**Query routing:** Structural queries (callers, imports, deps) -> `code_graph_query`. Semantic/concept queries -> CocoIndex (`mcp__cocoindex_code__search`). Session/memory queries -> `memory_context`.
   798	
   799	**CocoIndex seed bridge:** CocoIndex search results (file + line range) are accepted as seeds by `code_graph_context`, which resolves them to graph nodes and expands structurally. This combines "what resembles what" (CocoIndex) with "what connects to what" (Code Graph).
   800	
   801	**CCC tools** (CocoIndex lifecycle):

exec
/bin/zsh -lc "find .opencode/specs/system-spec-kit/026-graph-and-context-optimization -maxdepth 4 \\( -name 'implementation-summary.md' -o -name 'spec.md' \\) | rg 'graph|context|coco|fts|search|routing|cascade|optimization' | head -80" in /Users/michelkerkmeester/MEGA/Development/Code_Environment/Public
 succeeded in 0ms:
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/003-advisor-standards-alignment/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/003-advisor-standards-alignment/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-skill-graph-metadata-routing-boosts/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-skill-graph-metadata-routing-boosts/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-memory-search-routing-tuning/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/005-advisor-setup-command/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/005-advisor-setup-command/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-documentation-code-alignment/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-documentation-code-alignment/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/004-advisor-hook-surface-integration/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/004-advisor-hook-surface-integration/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/003-smart-remediation-opencode-plugin/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/003-smart-remediation-opencode-plugin/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/002-advisor-phrase-booster-tuning/implementation-summary.md
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.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-deferred-remediation-telemetry-run/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/001-deferred-remediation-telemetry-run/spec.md
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.opencode/specs/system-spec-kit/026-graph-and-context-optimization/006-skill-advisor/002-skill-graph-daemon-native-advisor-tools/implementation-summary.md
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.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/003-contextador/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/spec.md
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.opencode/specs/system-spec-kit/026-graph-and-context-optimization/001-research-and-baseline/001-claude-optimization-settings/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/002-code-graph-phase-runner-and-detect-changes/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/002-code-graph-phase-runner-and-detect-changes/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/007-review-remediation/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/007-review-remediation/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/004-skill-advisor-affordance-evidence/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/004-skill-advisor-affordance-evidence/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/005-memory-causal-trust-display/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/005-memory-causal-trust-display/spec.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/006-docs-and-catalogs-rollup/implementation-summary.md
.opencode/specs/system-spec-kit/026-graph-and-context-optimization/010-graph-impact-and-affordance-uplift/006-docs-and-catalogs-rollup/spec.md

codex
Search system has three layers, not one:

1. **Spec Kit Memory search**
   `memory_context()` is the preferred entry point, with `memory_search()` as the lower-level hybrid retrieval API. It uses vector, FTS5, BM25, causal graph, and degree channels, then runs 4 stages: candidate generation, fusion, rerank, filtering.
   See [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/README.md:363), [SKILL.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/SKILL.md:566), and [search README](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:36).

2. **Code Graph**
   Structural search: callers, imports, outlines, blast radius, graph neighborhoods. Default routing says structural queries go here before semantic search.
   See [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/README.md:508) and [SKILL.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/SKILL.md:775).

3. **CocoIndex**
   Semantic code search: “find code that does X”, similar implementations, unfamiliar modules. It bridges into Code Graph via seed results, but current session startup reported CocoIndex as missing.
   See [mcp-coco-index/SKILL.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/mcp-coco-index/SKILL.md:10) and [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/README.md:562).

Core code entry points:

- [memory-context.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:13): unified retrieval routing, intent detection, Code Graph context hooks.
- [memory-search.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:11): main `memory_search` handler, pipeline execution, telemetry, cache, feedback.
- [orchestrator.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/orchestrator.ts:46): 4-stage pipeline controller.
- [stage1-candidate-gen.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:6): raw retrieval from vector, hybrid, multi-concept, expansion paths.
- [stage2-fusion.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:6): single scoring point for session boost, recency, causal boost, graph signals, intent weights, feedback.

Relevant spec packets:

- [010-search-retrieval-quality-fixes](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/010-search-retrieval-quality-fixes/implementation-summary.md:40): fixed retrieval quality around context routing, folder recovery, token budgets, and intent confidence.
- [013-fts5-fix-and-search-dashboard](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/013-fts5-fix-and-search-dashboard/implementation-summary.md:45): fixed FTS5 multi-word quoting, DB path drift, search dashboard grouping, and silent failure logging.
- [026 graph/context optimization](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/026-graph-and-context-optimization/005-code-graph/implementation-summary.md): broader Code Graph and routing work.

My read: the live architecture is “graph-first for structure, CocoIndex for semantic code, Memory for session/spec history,” with Memory search internally using a 5-channel hybrid pipeline.
hook: Stop
hook: Stop Completed
2026-04-26T18:23:16.914973Z ERROR codex_core::session: failed to record rollout items: thread 019dcb07-18af-7bd1-a216-12b3619908be not found
tokens used
128,295
Search system has three layers, not one:

1. **Spec Kit Memory search**
   `memory_context()` is the preferred entry point, with `memory_search()` as the lower-level hybrid retrieval API. It uses vector, FTS5, BM25, causal graph, and degree channels, then runs 4 stages: candidate generation, fusion, rerank, filtering.
   See [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/README.md:363), [SKILL.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/SKILL.md:566), and [search README](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/README.md:36).

2. **Code Graph**
   Structural search: callers, imports, outlines, blast radius, graph neighborhoods. Default routing says structural queries go here before semantic search.
   See [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/README.md:508) and [SKILL.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/SKILL.md:775).

3. **CocoIndex**
   Semantic code search: “find code that does X”, similar implementations, unfamiliar modules. It bridges into Code Graph via seed results, but current session startup reported CocoIndex as missing.
   See [mcp-coco-index/SKILL.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/mcp-coco-index/SKILL.md:10) and [README.md](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/README.md:562).

Core code entry points:

- [memory-context.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-context.ts:13): unified retrieval routing, intent detection, Code Graph context hooks.
- [memory-search.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/handlers/memory-search.ts:11): main `memory_search` handler, pipeline execution, telemetry, cache, feedback.
- [orchestrator.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/orchestrator.ts:46): 4-stage pipeline controller.
- [stage1-candidate-gen.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage1-candidate-gen.ts:6): raw retrieval from vector, hybrid, multi-concept, expansion paths.
- [stage2-fusion.ts](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/skills/system-spec-kit/mcp_server/lib/search/pipeline/stage2-fusion.ts:6): single scoring point for session boost, recency, causal boost, graph signals, intent weights, feedback.

Relevant spec packets:

- [010-search-retrieval-quality-fixes](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/010-search-retrieval-quality-fixes/implementation-summary.md:40): fixed retrieval quality around context routing, folder recovery, token budgets, and intent confidence.
- [013-fts5-fix-and-search-dashboard](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/023-hybrid-rag-fusion-refinement/013-fts5-fix-and-search-dashboard/implementation-summary.md:45): fixed FTS5 multi-word quoting, DB path drift, search dashboard grouping, and silent failure logging.
- [026 graph/context optimization](/Users/michelkerkmeester/MEGA/Development/Code_Environment/Public/.opencode/specs/system-spec-kit/026-graph-and-context-optimization/005-code-graph/implementation-summary.md): broader Code Graph and routing work.

My read: the live architecture is “graph-first for structure, CocoIndex for semantic code, Memory for session/spec history,” with Memory search internally using a 5-channel hybrid pipeline.
