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false\n        },\n        \"content\": \"---\\ntitle: \\\"Rewrite Memory MCP README [system-spec-kit/022-hybrid-rag-fusion/016-rewrite-memory-mcp-readme/spec]\\\"\\ndescription: \\\"Complete rewrite of the Spec Kit Memory MCP server README to accurately document all 33 tools, hybrid search pipeline, and cognitive memory architecture.\\\"\\ntrigger_phrases:\\n  - \\\"mcp readme rewrite\\\"\\n  - \\\"016 mcp readme\\\"\\n  - \\\"memory mcp documentation\\\"\\n  - \\\"mcp server readme\\\"\\nimportance_tier: \\\"important\\\"\\ncontextType: \\\"implementation\\\"\\ntemplate_source_hint: \\\"<!-- SPECKIT_TEMPLATE_SOURCE: spec-core | v2.2 -->\\\"\\n_memory:\\n  continuity:\\n    packet_pointer: \\\"system-spec-kit/022-hybrid-rag-fusion/016-rewrite-memory-mcp-readme\\\"\\n    last_updated_at: \\\"2026-04-24T15:25:01Z\\\"\\n    last_updated_by: \\\"backfill-memory-block\\\"\\n    recent_action: \\\"Backfilled _memory block (repo-wide frontmatter sweep)\\\"\\n    next_safe_action: \\\"Revalidate packet docs and update continuity on next save\\\"\\n    key_files: [\\\"spec.md\\\"]\\n---\\n<!-- SPECKIT_LEVEL: 1 -->\\n# Specification: 016-rewrite-memory-mcp-readme\\n\\n<!-- SPECKIT_TEMPLATE_SOURCE: spec-core | v2.2 -->\\n\\n---\\n\\n<!-- ANCHOR:metadata -->\\n## 1. METADATA\\n\\n| Field | Value |\\n|-------|-------|\\n| **Level** | 1 |\\n| **Priority** | P1 |\\n| **Status** | In Progress (tasks tracker pending completion evidence) |\\n| **Created** | 2026-03-15 |\\n| **Branch** | `main` |\\n| **Parent** | `022-hybrid-rag-fusion` (Phase 016) |\\n| **Parent Spec** | ../spec.md |\\n| **Predecessor** | ../015-manual-testing-per-playbook/spec.md |\\n| **Successor** | ../017-update-install-guide/spec.md |\\n<!-- /ANCHOR:metadata -->\\n\\n---\\n\\n<!-- ANCHOR:problem -->\\n## 2. PROBLEM & PURPOSE\\n\\n### Problem Statement\\n\\nThe MCP server README (mcp_server/README.md, ~1281 lines) was written incrementally as features were added across 16 phases of the 022-hybrid-rag-fusion epic. It now mixes API reference, architecture, configuration, and troubleshooting concerns with no clear reader path. Some sections reference 28 tools when 33 exist. The hybrid search pipeline, cognitive memory (6-tier, 5-state, FSRS decay), and feature flag system are not cohesively documented.\\n\\n### Purpose\\n\\nProduce a complete rewrite grounded in the feature catalog that serves both newcomers (quick start, overview) and power users (full tool reference, architecture depth), with all 33 MCP tools accurately documented and DQI >= 75.\\n<!-- /ANCHOR:problem -->\\n\\n---\\n\\n<!-- ANCHOR:scope -->\\n## 3. SCOPE\\n\\n### In Scope\\n\\n| Category | Items |\\n|----------|-------|\\n| **Full rewrite** | `.opencode/skills/system-spec-kit/mcp_server/README.md` |\\n| **Section structure** | Overview, Quick Start, Architecture, MCP Tools (all 33), Search System, Configuration, Usage Examples, Troubleshooting, FAQ, Related Resources |\\n| **Content grounding** | Feature catalog (FEATURE_CATALOG.md) as authoritative source |\\n| **Quality gates** | DQI >= 75, no banned HVR words, template alignment with the README template |\\n\\n### Out of Scope\\n\\n- MCP server runtime code changes\\n- The install guide document (owned by sibling spec `017-update-install-guide`)\\n- Spec Kit README (owned by `018-rewrite-system-speckit-readme`)\\n- Command documentation (completed by `012-command-alignment`)\\n\\n### Files to Change\\n\\n| File Path | Change Type | Description |\\n|-----------|-------------|-------------|\\n| `.opencode/skills/system-spec-kit/mcp_server/README.md` | Rewrite | Complete rewrite from scratch using research brief and readme template |\\n| `.opencode/skills/system-spec-kit/mcp_server/README.md.bak` | Create | Backup of current README before rewrite |\\n<!-- /ANCHOR:scope -->\\n\\n---\\n\\n<!-- ANCHOR:requirements -->\\n## 4. REQUIREMENTS\\n\\n### P0 - Blockers (MUST complete)\\n\\n| ID | Requirement | Acceptance Criteria |\\n|----|-------------|---------------------|\\n| REQ-001 | All 33 MCP tools are documented (legacy `MR-001`) | Every tool in `TOOL_DEFINITIONS` appears with name, description, parameters, and layer annotation |\\n| REQ-002 | The rewrite is grounded in the feature catalog (legacy `MR-002`) | All 22 feature categories from the catalog are represented in relevant sections |\\n| REQ-003 | DQI is at least 75 (legacy `MR-003`) | `validate_document.py` scores the final document at 75 or above |\\n\\n### P1 - Required\\n\\n| ID | Requirement | Acceptance Criteria |\\n|----|-------------|---------------------|\\n| REQ-004 | The rewrite contains no banned HVR words (legacy `MR-004`) | Zero matches for sk-doc banned word list across the document |\\n| REQ-005 | The rewrite follows the README template structure (legacy `MR-005`) | Section headers match the active README template structure |\\n| REQ-006 | The intro is newcomer-friendly (legacy `MR-006`) | Overview and Quick Start sections are self-contained and require no prior knowledge |\\n| REQ-007 | The architecture section covers hybrid search (legacy `MR-007`) | The README describes BM25 plus vector fusion, FSRS decay, 6-tier importance, and the 5-state lifecycle |\\n| REQ-008 | Cross-references to sibling docs stay accurate (legacy `MR-008`) | Links to the install guide, the Spec Kit README, and command docs work without duplicating their content |\\n<!-- /ANCHOR:requirements -->\\n\\n---\\n\\n<!-- ANCHOR:success-criteria -->\\n## 5. SUCCESS CRITERIA\\n\\n- **SC-001**: All 33 tools documented with parameters and layer annotations\\n- **SC-002**: DQI >= 75 with zero banned HVR words\\n- **SC-003**: A newcomer can set up the MCP server using only Overview + Quick Start\\n- **SC-004**: A power user can find any tool's full parameter reference within 2 TOC clicks\\n\\n### Acceptance Scenarios\\n\\n**Given** the rewritten MCP README, **when** a reviewer audits it against `TOOL_DEFINITIONS`, **then** all 33 tools appear with the expected reference detail.\\n\\n**Given** a newcomer opens only the Overview and Quick Start sections, **when** they follow the guidance, **then** they can understand the MCP server and begin setup without outside context.\\n<!-- /ANCHOR:success-criteria -->\\n\\n---\\n\\n<!-- ANCHOR:risks -->\\n## 6. RISKS & DEPENDENCIES\\n\\n| Type | Item | Impact | Mitigation |\\n|------|------|--------|------------|\\n| Dependency | Feature catalog accuracy | High | Cross-reference catalog against `tool-schemas.ts` during research |\\n| Dependency | README template structure | Medium | Load the active template before drafting |\\n| Risk | Document too long for single-page reading | Medium | Use collapsible sections and clear TOC hierarchy |\\n| Risk | Tool descriptions duplicate command docs | Medium | Link to command docs for workflow details, keep README focused on reference |\\n<!-- /ANCHOR:risks -->\\n\\n---\\n\\n<!-- ANCHOR:questions -->\\n## 7. 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Constitutional memories apply globally. Saved context is scoped to a spec folder.\\n\\n**Q: What happens if I run `/memory:manage scan --force` on a large workspace?**\\n\\nThe scan re-indexes all previously indexed continuity artifacts and canonical spec docs regardless of whether their content has changed. This is slower than incremental scanning but useful after bulk renames or moves. For routine maintenance, omit `--force` to skip files whose content hash is unchanged.\\n\\n<!-- /ANCHOR:faq -->\\n\\n---\\n\\n<!-- ANCHOR:troubleshooting -->\\n## 8. TROUBLESHOOTING\",\n      \"start_line\": 298,\n      \"end_line\": 311,\n      \"score\": 0.6305865920066864,\n      \"raw_score\": 0.6305865920066864,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/skills/system-spec-kit/feature_catalog/02--mutation/01-memory-indexing-memorysave.md\",\n      \"language\": \"markdown\",\n      \"content\": \"# Memory indexing (memory_save)\\n\\n## 1. OVERVIEW\\n\\nCovers the save entry point that reads files, generates embeddings, applies quality gating and indexes content into the spec-doc record database.\\n\\nThis is how you add new knowledge to the system. You point it at a file and it reads, understands and stores the content so it becomes searchable. Before storing, it checks whether the same information already exists and decides whether to add it fresh, update an older version or skip it entirely. Quality checks catch low-value content before it clutters up the knowledge base.\\n\\n---\",\n      \"start_line\": 8,\n      \"end_line\": 16,\n      \"score\": 0.609700358776136,\n      \"raw_score\": 0.609700358776136,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/changelog/system-spec-kit/v2.4.0.0.md\",\n      \"language\": \"markdown\",\n      \"content\": \"- **Search API exposes more options** -- Three parameters that existed internally but were hidden from the tool interface are now available: tracking access history, including archived items, and selecting search mode.\\n- **Smarter embedding on updates** -- When a memory is updated, the system now generates its search embedding from the full title and content, not just the title. 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It now reuses that computation instead of doing it twice when constitutional memories (always-present rules) are involved.\\n- **Configurable similarity threshold** -- A function that detects \\\"interfering\\\" memories (ones too similar to each other) now accepts a custom threshold instead of using a fixed value.\",\n      \"start_line\": 39,\n      \"end_line\": 42,\n      \"score\": 0.593918799738475,\n      \"raw_score\": 0.593918799738475,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/skills/system-spec-kit/mcp_server/lib/search/vector-index-queries.ts\",\n      \"language\": \"typescript\",\n      \"content\": \"/* ───────────────────────────────────────────────────────────────\\n   RELATED MEMORIES AND USAGE TRACKING\\n----------------------------------------------------------------*/\\n\\n/**\\n * Gets memories related to a stored memory.\\n * @param memory_id - The memory identifier.\\n * @returns The related memory rows.\\n */\",\n      \"start_line\": 1040,\n      \"end_line\": 1048,\n      \"score\": 0.590979492754796,\n      \"raw_score\": 0.590979492754796,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \"README.md\",\n      \"language\": \"markdown\",\n      \"content\": \"### 🧠 Memory Engine\\n\\nThe 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.\\n\\n`/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.\",\n      \"start_line\": 334,\n      \"end_line\": 338,\n      \"score\": 0.586584885626463,\n      \"raw_score\": 0.586584885626463,\n      \"path_class\": \"docs\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/skills/system-spec-kit/mcp_server/INSTALL_GUIDE.md\",\n      \"language\": \"markdown\",\n      \"content\": \"### memory_search: Semantic Search\\n\\n`memory_search()` runs vector-based similarity search across all indexed memories.\\n\\n**Key parameters:**\\n- `query`: Natural language search query\\n- `limit`: Max results (default 10)\\n- `minState`: Minimum active memory state (HOT, WARM, COLD, DORMANT)\\n- `intent`: Task intent for weight adjustments (add_feature, fix_bug, refactor, etc.)\\n- `includeContent`: Embed full file content in results\\n\\n### memory_match_triggers: Fast Keyword Lookup\\n\\n`memory_match_triggers()` provides sub-50ms keyword-based matching. Use it for immediate context surfacing at the start of a conversation.\\n\\n### memory_save: Index a Continuity Source\\n\\n`memory_save()` indexes a single new or updated continuity-bearing document into the database. For bulk indexing, use `memory_index_scan()` instead.\",\n      \"start_line\": 640,\n      \"end_line\": 657,\n      \"score\": 0.5792145909425681,\n      \"raw_score\": 0.5792145909425681,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/skills/system-spec-kit/mcp_server/lib/search/surrogate-storage.ts\",\n      \"language\": \"typescript\",\n      \"content\": \"/* ───────────────────────────────────────────────────────────────\\n   3. STORE\\n----------------------------------------------------------------*/\\n\\n/**\\n * Store surrogate metadata for a memory document.\\n *\\n * Uses INSERT OR REPLACE to handle re-indexing gracefully.\\n * NOTE: Feature flag guard is the caller's responsibility.\\n *\\n * @param db        - SQLite database instance.\\n * @param memoryId  - ID of the memory document.\\n * @param surrogates - Generated surrogate metadata.\\n */\",\n      \"start_line\": 72,\n      \"end_line\": 85,\n      \"score\": 0.5786095076865774,\n      \"raw_score\": 0.5786095076865774,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/skills/sk-deep-review/SKILL.md\",\n      \"language\": \"markdown\",\n      \"content\": \"### Core Innovation: Fresh Context Per Iteration\\n\\nEach agent dispatch gets a fresh context window. State continuity comes from files, not memory. This solves context degradation in long review sessions where accumulated findings would otherwise bias subsequent dimensions.\\n\\n### Data Flow\",\n      \"start_line\": 321,\n      \"end_line\": 325,\n      \"score\": 0.5745943451309738,\n      \"raw_score\": 0.5745943451309738,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/skills/system-spec-kit/mcp_server/lib/storage/reconsolidation.ts\",\n      \"language\": \"typescript\",\n      \"content\": \"// ───────────────────────────────────────────────────────────────\\n// 8. COMPLEMENT OPERATION\\n\\n// ───────────────────────────────────────────────────────────────\\n/**\\n * Store a new memory unchanged (similarity < 0.75).\\n *\\n * The new memory is distinct enough from existing memories to be\\n * stored as a separate entry.\\n *\\n * @param newMemory - The new memory to store\\n * @param storeMemory - Callback to store the memory\\n * @param topSimilarity - The highest similarity score found (null if no candidates)\\n * @returns ComplementResult with storage details\\n */\",\n      \"start_line\": 605,\n      \"end_line\": 619,\n      \"score\": 0.5727674704795547,\n      \"raw_score\": 0.5727674704795547,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    },\n    {\n      \"file_path\": \".gemini/changelog/system-spec-kit/v3.0.0.0.md\",\n      \"language\": \"markdown\",\n      \"content\": \"## What Changed: Phase by Phase\\n\\n#### Phases 1-9: Building the search and storage engine\\n\\n- **Phase 1 (program coordination)** -- Defined the overall architecture and established the 5-channel, 4-stage pipeline as the single production search path, replacing earlier isolated experiments.\\n- **Phase 2 (indexing normalization)** -- Fixed duplicate indexing problems. The same document could be indexed multiple times under different paths or broken into overlapping sections. Now each artifact is indexed exactly once.\\n- **Phase 3 (constitutional memory manager)** -- Rebuilt the `/memory:learn` command from a simple \\\"create a rule\\\" tool into a full manager with list, edit, remove, and budget controls. Constitutional memories get a 3x search boost and never decay over time.\",\n      \"start_line\": 32,\n      \"end_line\": 38,\n      \"score\": 0.5632253812504171,\n      \"raw_score\": 0.5632253812504171,\n      \"path_class\": \"implementation\",\n      \"rankingSignals\": []\n    }\n  ],\n  \"total_returned\": 10,\n  \"offset\": 0,\n  \"dedupedAliases\": 28,\n  \"uniqueResultCount\": 10,\n  \"message\": null\n}","metadata":{"truncated":false},"title":"","time":{"start":1777300360091,"end":1777300360300},"attachments":[]}}}
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{"type":"step_start","timestamp":1777300363616,"sessionID":"ses_230a516f9ffeRAMGp9K4KB56TA","part":{"id":"prt_dcf5b595c001awmpGJJN71EUnn","messageID":"msg_dcf5b4e88001hl7vGsPhKdZ3bm","sessionID":"ses_230a516f9ffeRAMGp9K4KB56TA","snapshot":"4363a3a385037fcf91a8287ec5f4d374ab404a4b","type":"step-start"}}
{"type":"text","timestamp":1777300387380,"sessionID":"ses_230a516f9ffeRAMGp9K4KB56TA","part":{"id":"prt_dcf5b65e6001IacYw7qT8OHnYI","messageID":"msg_dcf5b4e88001hl7vGsPhKdZ3bm","sessionID":"ses_230a516f9ffeRAMGp9K4KB56TA","type":"text","text":"Here's what I found about **memory** in this codebase:\n\n## 🧠 Spec Kit Memory System\n\nThe central memory system is a **local-first cognitive memory MCP server** (referenced in `README.md:334`). It provides:\n\n### Core Layers\n| Layer | Tools | Purpose |\n|-------|-------|---------|\n| **L1 Orchestration** | `memory_context`, `session_bootstrap`, `session_resume` | Unified entry point, session recovery |\n| **L2 Core** | `memory_search`, `memory_quick_search`, `memory_match_triggers`, `memory_save` | Semantic/lexical search, trigger matching, indexing |\n| **L3 Discovery** | `memory_list`, `memory_stats`, `memory_health` | Browsing, stats, health diagnostics |\n| **L4 Mutation** | `memory_delete`, `memory_update`, `memory_validate`, `memory_bulk_delete` | CRUD operations, validation feedback |\n| **L5 Lifecycle** | `checkpoint_create/list/restore/delete` | Snapshot/restore |\n| **L6 Analysis** | `memory_drift_why`, `memory_causal_link/stats`, `task_preflight/postflight`, `code_graph_query` | Causal tracing, learning deltas, structural queries |\n| **L7 Maintenance** | `memory_index_scan`, `code_graph_scan`, `memory_ingest_*`, `memory_get_learning_history` | Bulk indexing, graph scanning |\n| **L8 Skill Advisor** | `advisor_recommend/status/validate` | Skill routing |\n| **L9 Coverage Graph** | `deep_loop_graph_*` | Deep research/review coverage tracking |\n\n### Architecture\n- **Hybrid RAG Fusion**: Vector embeddings + BM25 + FTS5 full-text search with cross-encoder reranking\n- **6-tier importance**: constitutional → critical → important → normal → temporary → deprecated\n- **5-state lifecycle**: HOT → WARM → COLD → DORMANT → ARCHIVED with FSRS decay\n- **Causal graph**: tracks decision lineage (`caused`, `enabled`, `supersedes`, `contradicts`, etc.)\n- **Cognitive features**: attention-based decay, co-activation, session deduplication, surge protection\n\n### Key Files\n| Path | Description |\n|------|-------------|\n| `.opencode/skills/system-spec-kit/mcp_server/` | MCP server implementation |\n| `.opencode/skills/system-spec-kit/references/memory/memory_system.md` | Memory system reference doc |\n| `.opencode/specs/system-spec-kit/022-hybrid-rag-fusion/` | 16+ phases of memory upgrade specs |\n| `.opencode/skills/system-spec-kit/constitutional/` | Constitutional memory rules |\n\n### Major Spec Folders\n- `022-hybrid-rag-fusion` — 16 phases covering search pipeline, indexing, cognitive memory, tool schemas\n- `024-compact-code-graph` — Code graph integration with memory\n- `016-rewrite-memory-mcp-readme` — Full README rewrite for all 33 MCP tools\n\nThe memory system has ~85+ test files (`memory-*.vitest.ts`) and extensive manual testing playbooks across 19 categories.","time":{"start":1777300387379,"end":1777300387379}}}
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