docs(04-04): complete CLI query interface plan

Tasks completed: 2/2
- Add query action routing to stdin handler
- Add usage documentation as code comment

SUMMARY: .planning/phases/04-semantic-intelligence/04-04-SUMMARY.md

.planning/STATE.md

@@ -10,18 +10,18 @@ See: .planning/PROJECT.md (updated 2026-01-19)
 ## Current Position
 
 Phase: 4 of 4 (Semantic Intelligence & Scale)
-Plan: 3 of 3 complete
+Plan: 4 of 4 complete
 Status: Phase complete
-Last activity: 2026-01-20 — Completed 04-02-PLAN.md (Query Interface) and 04-03-PLAN.md (Entity Generation Instructions)
+Last activity: 2026-01-20 — Completed 04-04-PLAN.md (CLI Query Interface - gap closure)
 
 Progress: [██████████] 100%
 
 ## Performance Metrics
 
 **Velocity:**
-- Total plans completed: 10
-- Average duration: 2.5 min
-- Total execution time: 25 min
+- Total plans completed: 11
+- Average duration: 2.6 min
+- Total execution time: 29 min
 
 **By Phase:**
 
@@ -30,7 +30,7 @@ Progress: [██████████] 100%
 | 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 | 3/3 | 8 min | 2.7 min |
+| 4. Semantic Intelligence | 4/4 | 12 min | 3.0 min |
 
 *Updated after each plan completion*
 
@@ -64,6 +64,9 @@ Progress: [██████████] 100%
 | LEFT JOIN allows forward references | 04-02 | Edges can exist before target nodes indexed |
 | UNION in recursive CTE | 04-02 | Prevents infinite loops in cyclic graphs |
 | maxDepth default of 5 | 04-02 | Prevents runaway queries on deep dependencies |
+| Query mode read-only | 04-04 | Query actions don't persist to disk, safe operations |
+| Default limit 10 for dependents | 04-04 | Prevents huge output for files with many dependents |
+| Query routing before Write/Edit | 04-04 | Clean separation between query and indexing modes |
 
 ### Pending Todos
 
@@ -76,7 +79,7 @@ Progress: [██████████] 100%
 ## Session Continuity
 
 Last session: 2026-01-20
-Stopped at: Completed 04-02-PLAN.md and 04-03-PLAN.md
+Stopped at: Completed 04-04-PLAN.md (CLI Query Interface gap closure)
 Resume file: None
 
 ## Phase Progress
@@ -90,3 +93,4 @@ Resume file: None
 - 04-01: SQLite graph layer ✓
 - 04-02: Query interface ✓
 - 04-03: Entity generation instructions ✓
+- 04-04: CLI query interface (gap closure) ✓

.planning/phases/04-semantic-intelligence/04-04-SUMMARY.md

@@ -0,0 +1,101 @@
+---
+phase: 04-semantic-intelligence
+plan: 04
+subsystem: codebase-intelligence
+tags: [sql.js, graph-queries, cli-interface, dependency-analysis]
+
+# Dependency graph
+requires:
+  - phase: 04-01
+    provides: SQLite graph database with nodes and edges tables
+  - phase: 04-02
+    provides: getDependents() and getHotspots() query functions
+provides:
+  - CLI query interface via stdin for graph database queries
+  - handleQuery() routing function for dependents and hotspots queries
+  - JSON output to stdout for Claude consumption
+affects: [codebase-analysis, dependency-tracking, refactoring-safety]
+
+# Tech tracking
+tech-stack:
+  added: []
+  patterns: [stdin-json-routing, query-action-pattern]
+
+key-files:
+  created: []
+  modified: [hooks/gsd-intel-index.js]
+
+key-decisions:
+  - "Query mode does not persist to disk (read-only operations)"
+  - "Default limit of 10 for dependents prevents huge output"
+  - "Query action routing occurs before Write/Edit handling in stdin handler"
+
+patterns-established:
+  - "Query action pattern: {action: 'query', type: 'dependents'|'hotspots', ...options}"
+  - "JSON error objects returned to stdout for graceful error handling"
+
+# Metrics
+duration: 4min
+completed: 2026-01-20
+---
+
+# Phase 04 Plan 04: CLI Query Interface Summary
+
+**CLI query interface exposes getDependents() and getHotspots() via stdin, enabling Claude to answer "what uses this file?" questions**
+
+## Performance
+
+- **Duration:** 4 min
+- **Started:** 2026-01-20T16:10:00Z
+- **Completed:** 2026-01-20T16:14:00Z
+- **Tasks:** 2
+- **Files modified:** 1
+
+## Accomplishments
+- getDependents() function now accessible via CLI (no longer orphaned)
+- Query interface accepts JSON actions via stdin and returns results to stdout
+- Support for both dependents queries (transitive "what uses this?") and hotspots queries (most depended-on files)
+- Complete error handling for missing parameters and unknown query types
+
+## Task Commits
+
+Each task was committed atomically:
+
+1. **Task 1: Add query action routing to stdin handler** - `f46327a` (feat)
+2. **Task 2: Add usage documentation as code comment** - `791265a` (docs)
+
+## Files Created/Modified
+- `hooks/gsd-intel-index.js` - Added handleQuery() function and stdin routing for query actions, plus CLI usage documentation
+
+## Decisions Made
+
+**Query mode read-only:** Query actions do not persist to disk. The database is opened, queried, and closed without writes. This keeps query operations safe and lightweight.
+
+**Default limits:** Dependents queries default to 10 results, hotspots to 5. This prevents overwhelming output when a file has many dependents. Clients can override via `limit` parameter.
+
+**Routing priority:** Query actions are handled before Write/Edit tool processing in the stdin handler. This ensures clean separation between query mode and indexing mode.
+
+## Deviations from Plan
+
+None - plan executed exactly as written.
+
+## Issues Encountered
+
+None
+
+## User Setup Required
+
+None - no external service configuration required.
+
+## Next Phase Readiness
+
+**Gap closure complete.** INTEL-05 verification is now unblocked:
+- getDependents() is callable via CLI query interface
+- Graph database queries work end-to-end (stdin → query → stdout)
+- Claude can query dependency information during sessions
+
+The semantic intelligence system is complete and ready for production use.
+
+---
+*Phase: 04-semantic-intelligence*
+*Completed: 2026-01-20*