docs(04-01): complete SQLite graph layer plan
Tasks completed: 3/3 - Add sql.js dependency and graph schema - Implement graph database helpers - Sync entity files to graph on write SUMMARY: .planning/phases/04-semantic-intelligence/04-01-SUMMARY.md Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Lex Christopherson
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.planning/STATE.md
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# Project State
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## Project Reference
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See: .planning/PROJECT.md (updated 2026-01-19)
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**Core value:** Claude understands your codebase structure and conventions before it starts working — automatically
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**Current focus:** v1.9.0 Codebase Intelligence System
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## Current Position
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Phase: 4 of 4 (Semantic Intelligence & Scale)
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Plan: 1 of 3 complete
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Status: In progress
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Last activity: 2026-01-20 — Completed 04-01-PLAN.md (SQLite graph layer)
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Progress: [████████░░] 80%
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## Performance Metrics
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**Velocity:**
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- Total plans completed: 8
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- Average duration: 2.5 min
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- Total execution time: 21 min
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**By Phase:**
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| Phase | Plans | Total | Avg/Plan |
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|-------|-------|-------|----------|
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| 1. Foundation & Learning | 2/2 | 7 min | 3.5 min |
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| 2. Context Injection | 2/2 | 4 min | 2.0 min |
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| 3. Brownfield & Integration | 3/3 | 6 min | 2.0 min |
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| 4. Semantic Intelligence | 1/3 | 4 min | 4.0 min |
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*Updated after each plan completion*
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## Accumulated Context
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### Decisions
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| Decision | Phase | Rationale |
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|----------|-------|-----------|
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| index.json keyed by absolute path | 01-01 | O(1) lookup for file entries |
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| JSON schema with version field | 01-01 | Enables future schema migrations |
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| updated=null for initialization | 01-01 | Distinguishes init from update |
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| Use heredoc for stdin testing | 01-02 | Pipe chaining has timing issues with async stdin |
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| Extract 'default' as export name | 01-02 | Both 'default' and identifier recorded for default exports |
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| Read file from disk for Edit tool | 01-02 | Edit only provides old_string/new_string, not full content |
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| Regenerate conventions every index update | 02-01 | Detection is fast, avoids staleness issues |
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| Skip 'default' in case detection | 02-01 | Keyword, not naming convention indicator |
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| Single lowercase words as camelCase | 02-01 | Follows camelCase rules (e.g., 'main', 'app') |
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| Use lookup tables for purposes | 02-01 | More maintainable than regex patterns |
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| Target < 500 tokens for summary | 02-02 | Minimize context window usage |
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| Top 5 directories, top 3 suffixes | 02-02 | Keep output concise |
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| Command documents same regex as hook | 03-01 | Consistency between bulk scan and incremental updates |
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| generateSummary in intel-index.js | 03-01 | Co-locate all intel generation; regenerate on every update |
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| No FK constraints in graph schema | 04-01 | Entities can reference before target indexed |
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| Virtual id from JSON body | 04-01 | Flexible node structure with unique constraint |
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| Delete-then-insert for edges | 04-01 | Clean replacement removes stale links |
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| Singleton WASM instance | 04-01 | Avoids repeated sql.js init overhead |
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### Pending Todos
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- `/gsd:resume-work` decimal phase handling (deferred from v1.8.0)
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### Blockers/Concerns
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- `.planning/` is gitignored in GSD repo - intel files created but not committed (expected for project-local data)
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## Session Continuity
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Last session: 2026-01-20
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Stopped at: Completed 04-01-PLAN.md
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Resume file: None
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## Phase Progress
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- Phase 1: Foundation & Learning ✓
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- Phase 2: Context Injection ✓
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- Phase 3: Brownfield & Integration ✓
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- Phase 4: Semantic Intelligence & Scale ◐ (1/3 plans complete)
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**Phase 4 status:**
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- 04-01: SQLite graph layer ✓
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- 04-02: Query interface ○
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- 04-03: Integration ○
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.planning/phases/04-semantic-intelligence/04-01-SUMMARY.md
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---
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phase: 04-semantic-intelligence
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plan: 01
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subsystem: database
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tags: [sqlite, sql.js, wasm, graph-database, entity-relationships]
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requires:
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- phase: 03-brownfield-integration
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provides: entity file system and summary regeneration
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provides:
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- SQLite graph database for entity relationships
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- Node/edge schema for semantic queries
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- Automatic graph sync on entity writes
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affects: [04-02 query interface, future blast-radius queries]
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tech-stack:
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added: [sql.js ^1.12.0]
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patterns: [simple-graph schema, WASM singleton, async-then-sync operations]
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key-files:
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created: []
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modified: [hooks/gsd-intel-index.js, package.json]
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key-decisions:
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- "No FOREIGN KEY constraints - entities can reference before target indexed"
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- "Virtual id column from JSON body for flexible node structure"
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- "Delete-then-insert for edge updates (clean replacement)"
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- "Singleton WASM instance to avoid repeated init overhead"
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patterns-established:
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- "Graph sync before summary regeneration"
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- "Silent failure pattern for non-blocking operations"
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duration: 4min
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completed: 2026-01-20
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---
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# Phase 4 Plan 1: SQLite Graph Layer Summary
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**SQLite graph database using sql.js WASM for entity relationship storage and querying**
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## Performance
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- **Duration:** 4 min
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- **Started:** 2026-01-20T09:45:00Z
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- **Completed:** 2026-01-20T09:53:00Z
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- **Tasks:** 3
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- **Files modified:** 2
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## Accomplishments
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- Added sql.js WASM SQLite dependency for zero-native-dependency graph storage
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- Implemented simple-graph schema with nodes (JSON body) and edges (source/target/relationship)
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- Graph database helpers for load, persist, and singleton WASM management
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- Entity files now sync to graph database on every write, creating nodes and edges from wiki-links
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## Task Commits
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Each task was committed atomically:
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1. **Task 1: Add sql.js dependency and graph schema** - `11ab4a9` (feat)
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2. **Task 2: Implement graph database helpers** - `ec038e7` (feat)
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3. **Task 3: Sync entity to graph on write** - `a39988e` (feat)
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## Files Created/Modified
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- `package.json` - Added sql.js ^1.12.0 dependency
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- `hooks/gsd-intel-index.js` - GRAPH_SCHEMA constant, loadGraphDatabase(), persistDatabase(), getSQL(), syncEntityToGraph()
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## Decisions Made
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- **No FOREIGN KEY constraints:** Entity A can reference entity B before B is indexed. Orphan edges are acceptable and expected in incremental indexing workflows.
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- **Virtual id column:** Uses `json_extract(body, '$.id')` for flexible node structure while maintaining unique constraint for upserts.
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- **Delete-then-insert for edges:** Clean replacement of all outgoing edges on entity update ensures stale links are removed.
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- **Singleton WASM instance:** sql.js WASM init is expensive; caching the SQL constructor avoids repeated overhead across hook invocations within same process.
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## Deviations from Plan
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None - plan executed exactly as written.
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## Issues Encountered
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None.
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## User Setup Required
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None - no external service configuration required.
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## Next Phase Readiness
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- Graph database infrastructure complete
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- Ready for query interface implementation (Plan 04-02)
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- Schema supports "what depends on X" and "what does X depend on" queries
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---
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*Phase: 04-semantic-intelligence*
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*Completed: 2026-01-20*
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