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+# Project State
+
+## Project Reference
+
+See: .planning/PROJECT.md (updated 2026-01-19)
+
+**Core value:** Claude understands your codebase structure and conventions before it starts working — automatically
+**Current focus:** v1.9.0 Codebase Intelligence System
+
+## Current Position
+
+Phase: 4 of 4 (Semantic Intelligence & Scale)
+Plan: 1 of 3 complete
+Status: In progress
+Last activity: 2026-01-20 — Completed 04-01-PLAN.md (SQLite graph layer)
+
+Progress: [████████░░] 80%
+
+## Performance Metrics
+
+**Velocity:**
+- Total plans completed: 8
+- Average duration: 2.5 min
+- Total execution time: 21 min
+
+**By Phase:**
+
+| Phase | Plans | Total | Avg/Plan |
+|-------|-------|-------|----------|
+| 1. Foundation & Learning | 2/2 | 7 min | 3.5 min |
+| 2. Context Injection | 2/2 | 4 min | 2.0 min |
+| 3. Brownfield & Integration | 3/3 | 6 min | 2.0 min |
+| 4. Semantic Intelligence | 1/3 | 4 min | 4.0 min |
+
+*Updated after each plan completion*
+
+## Accumulated Context
+
+### Decisions
+
+| Decision | Phase | Rationale |
+|----------|-------|-----------|
+| index.json keyed by absolute path | 01-01 | O(1) lookup for file entries |
+| JSON schema with version field | 01-01 | Enables future schema migrations |
+| updated=null for initialization | 01-01 | Distinguishes init from update |
+| Use heredoc for stdin testing | 01-02 | Pipe chaining has timing issues with async stdin |
+| Extract 'default' as export name | 01-02 | Both 'default' and identifier recorded for default exports |
+| Read file from disk for Edit tool | 01-02 | Edit only provides old_string/new_string, not full content |
+| Regenerate conventions every index update | 02-01 | Detection is fast, avoids staleness issues |
+| Skip 'default' in case detection | 02-01 | Keyword, not naming convention indicator |
+| Single lowercase words as camelCase | 02-01 | Follows camelCase rules (e.g., 'main', 'app') |
+| Use lookup tables for purposes | 02-01 | More maintainable than regex patterns |
+| Target < 500 tokens for summary | 02-02 | Minimize context window usage |
+| Top 5 directories, top 3 suffixes | 02-02 | Keep output concise |
+| Command documents same regex as hook | 03-01 | Consistency between bulk scan and incremental updates |
+| generateSummary in intel-index.js | 03-01 | Co-locate all intel generation; regenerate on every update |
+| No FK constraints in graph schema | 04-01 | Entities can reference before target indexed |
+| Virtual id from JSON body | 04-01 | Flexible node structure with unique constraint |
+| Delete-then-insert for edges | 04-01 | Clean replacement removes stale links |
+| Singleton WASM instance | 04-01 | Avoids repeated sql.js init overhead |
+
+### Pending Todos
+
+- `/gsd:resume-work` decimal phase handling (deferred from v1.8.0)
+
+### Blockers/Concerns
+
+- `.planning/` is gitignored in GSD repo - intel files created but not committed (expected for project-local data)
+
+## Session Continuity
+
+Last session: 2026-01-20
+Stopped at: Completed 04-01-PLAN.md
+Resume file: None
+
+## Phase Progress
+
+- Phase 1: Foundation & Learning ✓
+- Phase 2: Context Injection ✓
+- Phase 3: Brownfield & Integration ✓
+- Phase 4: Semantic Intelligence & Scale ◐ (1/3 plans complete)
+
+**Phase 4 status:**
+- 04-01: SQLite graph layer ✓
+- 04-02: Query interface ○
+- 04-03: Integration ○
diff --git a/.planning/phases/04-semantic-intelligence/04-01-SUMMARY.md b/.planning/phases/04-semantic-intelligence/04-01-SUMMARY.md
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+---
+phase: 04-semantic-intelligence
+plan: 01
+subsystem: database
+tags: [sqlite, sql.js, wasm, graph-database, entity-relationships]
+
+requires:
+  - phase: 03-brownfield-integration
+    provides: entity file system and summary regeneration
+
+provides:
+  - SQLite graph database for entity relationships
+  - Node/edge schema for semantic queries
+  - Automatic graph sync on entity writes
+
+affects: [04-02 query interface, future blast-radius queries]
+
+tech-stack:
+  added: [sql.js ^1.12.0]
+  patterns: [simple-graph schema, WASM singleton, async-then-sync operations]
+
+key-files:
+  created: []
+  modified: [hooks/gsd-intel-index.js, package.json]
+
+key-decisions:
+  - "No FOREIGN KEY constraints - entities can reference before target indexed"
+  - "Virtual id column from JSON body for flexible node structure"
+  - "Delete-then-insert for edge updates (clean replacement)"
+  - "Singleton WASM instance to avoid repeated init overhead"
+
+patterns-established:
+  - "Graph sync before summary regeneration"
+  - "Silent failure pattern for non-blocking operations"
+
+duration: 4min
+completed: 2026-01-20
+---
+
+# Phase 4 Plan 1: SQLite Graph Layer Summary
+
+**SQLite graph database using sql.js WASM for entity relationship storage and querying**
+
+## Performance
+
+- **Duration:** 4 min
+- **Started:** 2026-01-20T09:45:00Z
+- **Completed:** 2026-01-20T09:53:00Z
+- **Tasks:** 3
+- **Files modified:** 2
+
+## Accomplishments
+
+- Added sql.js WASM SQLite dependency for zero-native-dependency graph storage
+- Implemented simple-graph schema with nodes (JSON body) and edges (source/target/relationship)
+- Graph database helpers for load, persist, and singleton WASM management
+- Entity files now sync to graph database on every write, creating nodes and edges from wiki-links
+
+## Task Commits
+
+Each task was committed atomically:
+
+1. **Task 1: Add sql.js dependency and graph schema** - `11ab4a9` (feat)
+2. **Task 2: Implement graph database helpers** - `ec038e7` (feat)
+3. **Task 3: Sync entity to graph on write** - `a39988e` (feat)
+
+## Files Created/Modified
+
+- `package.json` - Added sql.js ^1.12.0 dependency
+- `hooks/gsd-intel-index.js` - GRAPH_SCHEMA constant, loadGraphDatabase(), persistDatabase(), getSQL(), syncEntityToGraph()
+
+## Decisions Made
+
+- **No FOREIGN KEY constraints:** Entity A can reference entity B before B is indexed. Orphan edges are acceptable and expected in incremental indexing workflows.
+- **Virtual id column:** Uses `json_extract(body, '$.id')` for flexible node structure while maintaining unique constraint for upserts.
+- **Delete-then-insert for edges:** Clean replacement of all outgoing edges on entity update ensures stale links are removed.
+- **Singleton WASM instance:** sql.js WASM init is expensive; caching the SQL constructor avoids repeated overhead across hook invocations within same process.
+
+## Deviations from Plan
+
+None - plan executed exactly as written.
+
+## Issues Encountered
+
+None.
+
+## User Setup Required
+
+None - no external service configuration required.
+
+## Next Phase Readiness
+
+- Graph database infrastructure complete
+- Ready for query interface implementation (Plan 04-02)
+- Schema supports "what depends on X" and "what does X depend on" queries
+
+---
+*Phase: 04-semantic-intelligence*
+*Completed: 2026-01-20*