moflo 4.8.16 → 4.8.19

package/.claude/guidance/shipped/memory-strategy.md

@@ -1,204 +1,204 @@
-# Memory & Semantic Search Strategy
-
-**Purpose:** How memory, embeddings, and semantic search work in moflo. Reference when debugging memory issues, understanding the search pipeline, or configuring memory for a consumer project.
-
----
-
-## Architecture Overview
-
-```
-Source Files (.claude/guidance/, docs/)
-         |
-         v
-index-guidance.mjs (chunking, RAG linking)
-         |
-         v
-.swarm/memory.db (SQLite - entries + metadata)
-         |
-         v
-build-embeddings.mjs (384-dim neural or hash vectors)
-         |
-         v
-Search layer (cosine similarity - MCP, CLI, or script)
-```
-
----
-
-## Key Files
-
-| File | Purpose |
-|------|---------|
-| `.swarm/memory.db` | SQLite database with all entries, embeddings, metadata |
-| `.swarm/code-map-hash.txt` | SHA-256 hash for incremental code map skip |
-| `.claude-flow/neural/patterns.json` | ReasoningBank learned patterns |
-| `bin/build-embeddings.mjs` | Generates 384-dim embeddings |
-| `bin/index-guidance.mjs` | Indexes guidance files with RAG linking |
-| `bin/generate-code-map.mjs` | Generates structural code map (projects, dirs, types, interfaces) |
-
----
-
-## Embedding Strategy
-
-**Primary model:** `Xenova/all-MiniLM-L6-v2` (384-dim, neural — used by `build-embeddings.mjs`)
-**Fallback model:** `domain-aware-hash-v1` (384-dim, hash — used when Transformers.js unavailable)
-
-**Critical rule:** Query embeddings MUST match stored embeddings. Both the search scripts and MCP tools auto-detect the stored model and generate matching query vectors. Cross-model cosine similarity is meaningless.
-
-**Neural embeddings (primary):**
-- Uses `@xenova/transformers` with ONNX WASM runtime
-- True semantic understanding — "soft delete" matches "mark as deleted" without keyword overlap
-- ~3s for 1000 entries, loaded lazily and cached
-
-**Domain-aware hash (fallback):**
-- 12 domain clusters with project-specific terms
-- SimHash-style word encoding + bigram/trigram features
-- Good keyword-level matching, misses semantic paraphrases
-- No external dependencies — always available, <1s for 1000 entries
-
-See `guidance-memory-strategy.md` for full embedding pipeline details.
-
----
-
-## Search Commands
-
-All methods auto-detect the stored embedding model and generate matching query vectors:
-
-**MCP (Preferred):** `mcp__moflo__memory_search` — `query: "your query", namespace: "guidance"`
-
-**CLI (Fallback):**
-```bash
-npx flo memory search --query "your query" --namespace guidance
-```
-
-**Search options:**
-
-| Flag | Default | Purpose |
-|------|---------|---------|
-| `--namespace` | all | Filter to specific namespace |
-| `--limit` | 5 | Number of results |
-| `--threshold` | 0.3 | Minimum similarity score |
-| `--json` | false | Output as JSON |
-
-### Code Map Search (for codebase navigation)
-
-When you need to find where a type, service, entity, or component lives — search `code-map` BEFORE using Glob/Grep:
-
-**MCP:** `mcp__moflo__memory_search` — `query: "payment service", namespace: "code-map"`
-
-**What code-map contains:**
-
-| Chunk prefix | What it answers |
-|--------------|-----------------|
-| `project:` | "What's in the api project?" |
-| `dir:` | "What types are in the entities directory?" |
-| `iface-map:` | "What implements IPaymentService?" |
-| `type-index:` | "Where is Service defined?" |
-
-**Regenerate:**
-```bash
-npx flo-codemap          # Incremental (skips if unchanged)
-npx flo-codemap --force  # Full rebuild
-```
-
----
-
-## Database Schema
-
-```sql
-memory_entries (
-  id TEXT PRIMARY KEY,
-  key TEXT NOT NULL,           -- e.g., "chunk-guidance-core-0"
-  namespace TEXT,              -- "guidance", "patterns", "default"
-  content TEXT,                -- Full text content
-  embedding TEXT,              -- JSON array of 384 floats
-  embedding_model TEXT,        -- "Xenova/all-MiniLM-L6-v2" or "domain-aware-hash-v1"
-  embedding_dimensions INTEGER,-- 384
-  metadata TEXT,               -- JSON: parentDoc, chunkTitle, prevChunk, nextChunk, siblings
-  tags TEXT,                   -- JSON array
-  status TEXT,                 -- "active"
-  created_at INTEGER,
-  updated_at INTEGER
-)
-```
-
----
-
-## RAG Linking (metadata fields)
-
-Each chunk includes navigation metadata:
-
-| Field | Purpose |
-|-------|---------|
-| `parentDoc` | Key of full document (e.g., `doc-guidance-core`) |
-| `prevChunk` | Previous chunk key for sequential reading |
-| `nextChunk` | Next chunk key |
-| `siblings` | All chunk keys from same document |
-| `hierarchicalParent` | H2 parent for H3 chunks |
-| `hierarchicalChildren` | H3 children for H2 chunks |
-| `contextBefore` | Overlapping text from previous chunk (20%) |
-| `contextAfter` | Overlapping text from next chunk (20%) |
-
----
-
-## Namespaces
-
-| Namespace | Content | Notes |
-|-----------|---------|-------|
-| `guidance` | Indexed guidance and docs | Largest — includes bundled moflo guidance |
-| `code-map` | Structural codebase index (projects, directories, types, interfaces) | Search BEFORE Glob/Grep for navigation |
-| `patterns` | Learned patterns from sessions | Grows over time |
-| `default` | Misc stored data | Small |
-
----
-
-## Session Start Indexing
-
-On every session start, moflo automatically runs three background indexers:
-
-| Indexer | Command | Namespace | What it does |
-|---------|---------|-----------|--------------|
-| Guidance | `npx flo-index` | `guidance` | Chunks markdown, builds RAG links, generates embeddings |
-| Code Map | `npx flo-codemap` | `code-map` | Scans source for types, interfaces, directories |
-| Learning | `npx flo-learn` | `patterns` | Pattern research on codebase |
-
-These are configured in the `SessionStart` hook in `.claude/settings.json` (set up by `npx flo init`).
-
-Indexing is incremental by default — files whose content hash hasn't changed are skipped. Use `--force` to reindex everything.
-
----
-
-## Troubleshooting
-
-| Symptom | Cause | Fix |
-|---------|-------|-----|
-| Search returns irrelevant results | Query/stored embedding model mismatch | Auto-detected now; verify with `--verbose` flag |
-| Low similarity scores | Query doesn't match domain terms | Include domain keywords in query |
-| "Vector: No" in list | Entry lacks embedding | Run `npx flo-index --force` |
-| Entries not found after adding file | Indexer hasn't run yet | Run `npx flo-index` or restart session |
-| Bundled moflo guidance not indexed | Not installed as dependency | Only indexes when `node_modules/moflo/.claude/guidance/` exists |
-
----
-
-## Verification Commands
-
-```bash
-# Test semantic search
-npx flo memory search --query "database entity pattern" --namespace guidance
-
-# Force reindex all guidance
-npx flo-index --force
-
-# Force rebuild embeddings
-npx flo-index --force
-
-# Check entry count (requires better-sqlite3 or sql.js)
-npx flo memory list --namespace guidance --limit 0
-```
-
----
-
-## See Also
-
-- `.claude/guidance/guidance-memory-strategy.md` - RAG system tuning guide
-- `.claude/guidance/agent-bootstrap.md` - Subagent bootstrap guide
-- `.claude/guidance/moflo.md` - Full CLI/MCP reference
+# Memory & Semantic Search Strategy
+
+**Purpose:** How memory, embeddings, and semantic search work in moflo. Reference when debugging memory issues, understanding the search pipeline, or configuring memory for a consumer project.
+
+---
+
+## Architecture Overview
+
+```
+Source Files (.claude/guidance/, docs/)
+         |
+         v
+index-guidance.mjs (chunking, RAG linking)
+         |
+         v
+.swarm/memory.db (SQLite - entries + metadata)
+         |
+         v
+build-embeddings.mjs (384-dim neural or hash vectors)
+         |
+         v
+Search layer (cosine similarity - MCP, CLI, or script)
+```
+
+---
+
+## Key Files
+
+| File | Purpose |
+|------|---------|
+| `.swarm/memory.db` | SQLite database with all entries, embeddings, metadata |
+| `.swarm/code-map-hash.txt` | SHA-256 hash for incremental code map skip |
+| `.claude-flow/neural/patterns.json` | ReasoningBank learned patterns |
+| `bin/build-embeddings.mjs` | Generates 384-dim embeddings |
+| `bin/index-guidance.mjs` | Indexes guidance files with RAG linking |
+| `bin/generate-code-map.mjs` | Generates structural code map (projects, dirs, types, interfaces) |
+
+---
+
+## Embedding Strategy
+
+**Primary model:** `Xenova/all-MiniLM-L6-v2` (384-dim, neural — used by `build-embeddings.mjs`)
+**Fallback model:** `domain-aware-hash-v1` (384-dim, hash — used when Transformers.js unavailable)
+
+**Critical rule:** Query embeddings MUST match stored embeddings. Both the search scripts and MCP tools auto-detect the stored model and generate matching query vectors. Cross-model cosine similarity is meaningless.
+
+**Neural embeddings (primary):**
+- Uses `@xenova/transformers` with ONNX WASM runtime
+- True semantic understanding — "soft delete" matches "mark as deleted" without keyword overlap
+- ~3s for 1000 entries, loaded lazily and cached
+
+**Domain-aware hash (fallback):**
+- 12 domain clusters with project-specific terms
+- SimHash-style word encoding + bigram/trigram features
+- Good keyword-level matching, misses semantic paraphrases
+- No external dependencies — always available, <1s for 1000 entries
+
+See `guidance-memory-strategy.md` for full embedding pipeline details.
+
+---
+
+## Search Commands
+
+All methods auto-detect the stored embedding model and generate matching query vectors:
+
+**MCP (Preferred):** `mcp__moflo__memory_search` — `query: "your query", namespace: "guidance"`
+
+**CLI (Fallback):**
+```bash
+npx flo memory search --query "your query" --namespace guidance
+```
+
+**Search options:**
+
+| Flag | Default | Purpose |
+|------|---------|---------|
+| `--namespace` | all | Filter to specific namespace |
+| `--limit` | 5 | Number of results |
+| `--threshold` | 0.3 | Minimum similarity score |
+| `--json` | false | Output as JSON |
+
+### Code Map Search (for codebase navigation)
+
+When you need to find where a type, service, entity, or component lives — search `code-map` BEFORE using Glob/Grep:
+
+**MCP:** `mcp__moflo__memory_search` — `query: "payment service", namespace: "code-map"`
+
+**What code-map contains:**
+
+| Chunk prefix | What it answers |
+|--------------|-----------------|
+| `project:` | "What's in the api project?" |
+| `dir:` | "What types are in the entities directory?" |
+| `iface-map:` | "What implements IPaymentService?" |
+| `type-index:` | "Where is Service defined?" |
+
+**Regenerate:**
+```bash
+npx flo-codemap          # Incremental (skips if unchanged)
+npx flo-codemap --force  # Full rebuild
+```
+
+---
+
+## Database Schema
+
+```sql
+memory_entries (
+  id TEXT PRIMARY KEY,
+  key TEXT NOT NULL,           -- e.g., "chunk-guidance-core-0"
+  namespace TEXT,              -- "guidance", "patterns", "default"
+  content TEXT,                -- Full text content
+  embedding TEXT,              -- JSON array of 384 floats
+  embedding_model TEXT,        -- "Xenova/all-MiniLM-L6-v2" or "domain-aware-hash-v1"
+  embedding_dimensions INTEGER,-- 384
+  metadata TEXT,               -- JSON: parentDoc, chunkTitle, prevChunk, nextChunk, siblings
+  tags TEXT,                   -- JSON array
+  status TEXT,                 -- "active"
+  created_at INTEGER,
+  updated_at INTEGER
+)
+```
+
+---
+
+## RAG Linking (metadata fields)
+
+Each chunk includes navigation metadata:
+
+| Field | Purpose |
+|-------|---------|
+| `parentDoc` | Key of full document (e.g., `doc-guidance-core`) |
+| `prevChunk` | Previous chunk key for sequential reading |
+| `nextChunk` | Next chunk key |
+| `siblings` | All chunk keys from same document |
+| `hierarchicalParent` | H2 parent for H3 chunks |
+| `hierarchicalChildren` | H3 children for H2 chunks |
+| `contextBefore` | Overlapping text from previous chunk (20%) |
+| `contextAfter` | Overlapping text from next chunk (20%) |
+
+---
+
+## Namespaces
+
+| Namespace | Content | Notes |
+|-----------|---------|-------|
+| `guidance` | Indexed guidance and docs | Largest — includes bundled moflo guidance |
+| `code-map` | Structural codebase index (projects, directories, types, interfaces) | Search BEFORE Glob/Grep for navigation |
+| `patterns` | Learned patterns from sessions | Grows over time |
+| `default` | Misc stored data | Small |
+
+---
+
+## Session Start Indexing
+
+On every session start, moflo automatically runs three background indexers:
+
+| Indexer | Command | Namespace | What it does |
+|---------|---------|-----------|--------------|
+| Guidance | `npx flo-index` | `guidance` | Chunks markdown, builds RAG links, generates embeddings |
+| Code Map | `npx flo-codemap` | `code-map` | Scans source for types, interfaces, directories |
+| Learning | `npx flo-learn` | `patterns` | Pattern research on codebase |
+
+These are configured in the `SessionStart` hook in `.claude/settings.json` (set up by `npx flo init`).
+
+Indexing is incremental by default — files whose content hash hasn't changed are skipped. Use `--force` to reindex everything.
+
+---
+
+## Troubleshooting
+
+| Symptom | Cause | Fix |
+|---------|-------|-----|
+| Search returns irrelevant results | Query/stored embedding model mismatch | Auto-detected now; verify with `--verbose` flag |
+| Low similarity scores | Query doesn't match domain terms | Include domain keywords in query |
+| "Vector: No" in list | Entry lacks embedding | Run `npx flo-index --force` |
+| Entries not found after adding file | Indexer hasn't run yet | Run `npx flo-index` or restart session |
+| Bundled moflo guidance not indexed | Not installed as dependency | Only indexes when `node_modules/moflo/.claude/guidance/` exists |
+
+---
+
+## Verification Commands
+
+```bash
+# Test semantic search
+npx flo memory search --query "database entity pattern" --namespace guidance
+
+# Force reindex all guidance
+npx flo-index --force
+
+# Force rebuild embeddings
+npx flo-index --force
+
+# Check entry count (requires better-sqlite3 or sql.js)
+npx flo memory list --namespace guidance --limit 0
+```
+
+---
+
+## See Also
+
+- `.claude/guidance/guidance-memory-strategy.md` - RAG system tuning guide
+- `.claude/guidance/agent-bootstrap.md` - Subagent bootstrap guide
+- `.claude/guidance/moflo.md` - Full CLI/MCP reference