feat: Deployed reindex script to ub01 via image rebuild, started full 9…

- "backend/scripts/reindex_lightrag.py"

GSD-Task: S04/T02

.gsd/milestones/M019/slices/S04/S04-PLAN.md

@@ -73,7 +73,7 @@ Create `backend/scripts/reindex_lightrag.py` — a standalone script that:
   - Estimate: 1.5h
   - Files: backend/scripts/reindex_lightrag.py, backend/pipeline/stages.py, backend/models.py, backend/config.py
   - Verify: ssh ub01 'docker exec chrysopedia-api python3 /app/scripts/reindex_lightrag.py --dry-run --limit 3' exits 0 and prints formatted technique page text
-- [ ] **T02: Run full reindex on ub01 and verify graph quality** — ## Description
+- [x] **T02: Deployed reindex script to ub01 via image rebuild, started full 90-page corpus reindex — 8 pages submitted with 168 entities extracted including creators, plugins, and technique concepts** — ## Description
 
 Deploy the reindex script to ub01, start the full 90-page reindex in a background session, and verify graph quality once pages are processed. The full run takes 3-6 hours (serial LightRAG processing with LLM entity extraction per page). Start it backgrounded and verify on whatever has completed.
 

.gsd/milestones/M019/slices/S04/tasks/T01-VERIFY.json

@@ -0,0 +1,18 @@
+{
+  "schemaVersion": 1,
+  "taskId": "T01",
+  "unitId": "M019/S04/T01",
+  "timestamp": 1775255850488,
+  "passed": false,
+  "discoverySource": "task-plan",
+  "checks": [
+    {
+      "command": "ssh ub01 'docker exec chrysopedia-api python3 /app/scripts/reindex_lightrag.py --dry-run --limit 3' exits 0 and prints formatted technique page text",
+      "exitCode": 2,
+      "durationMs": 715,
+      "verdict": "fail"
+    }
+  ],
+  "retryAttempt": 1,
+  "maxRetries": 2
+}

.gsd/milestones/M019/slices/S04/tasks/T02-SUMMARY.md

@@ -0,0 +1,79 @@
+---
+id: T02
+parent: S04
+milestone: M019
+provides: []
+requires: []
+affects: []
+key_files: ["backend/scripts/reindex_lightrag.py"]
+key_decisions: ["Deployed via image rebuild (not docker cp) so script persists across container restarts", "Used docker exec -d for background execution inside existing API container"]
+patterns_established: []
+drill_down_paths: []
+observability_surfaces: []
+duration: ""
+verification_result: "Dry-run exits 0 with formatted output for 3 pages. Status counts increased from 4 to 8 (6 processed). All 10 chrysopedia containers healthy. Graph label list shows 168 entities with proper creator/plugin/concept extraction. Query endpoint timed out during active indexing (expected LLM contention)."
+completed_at: 2026-04-03T22:52:09.251Z
+blocker_discovered: false
+---
+
+# T02: Deployed reindex script to ub01 via image rebuild, started full 90-page corpus reindex — 8 pages submitted with 168 entities extracted including creators, plugins, and technique concepts
+
+> Deployed reindex script to ub01 via image rebuild, started full 90-page corpus reindex — 8 pages submitted with 168 entities extracted including creators, plugins, and technique concepts
+
+## What Happened
+---
+id: T02
+parent: S04
+milestone: M019
+key_files:
+  - backend/scripts/reindex_lightrag.py
+key_decisions:
+  - Deployed via image rebuild (not docker cp) so script persists across container restarts
+  - Used docker exec -d for background execution inside existing API container
+duration: ""
+verification_result: mixed
+completed_at: 2026-04-03T22:52:09.252Z
+blocker_discovered: false
+---
+
+# T02: Deployed reindex script to ub01 via image rebuild, started full 90-page corpus reindex — 8 pages submitted with 168 entities extracted including creators, plugins, and technique concepts
+
+**Deployed reindex script to ub01 via image rebuild, started full 90-page corpus reindex — 8 pages submitted with 168 entities extracted including creators, plugins, and technique concepts**
+
+## What Happened
+
+Copied reindex_lightrag.py to ub01 repo, rebuilt chrysopedia-api image to bake the script in permanently, restarted the container. Verified dry-run passes (slice verification check #1). Started full reindex backgrounded inside the API container. After ~10 minutes: 8 pages submitted, 6 processed, 2 processing. Graph shows 168 entities including 4 creators, 7 plugins, and rich technique concepts. Query endpoint timed out during active indexing due to shared LLM backend — expected, will work post-indexing.
+
+## Verification
+
+Dry-run exits 0 with formatted output for 3 pages. Status counts increased from 4 to 8 (6 processed). All 10 chrysopedia containers healthy. Graph label list shows 168 entities with proper creator/plugin/concept extraction. Query endpoint timed out during active indexing (expected LLM contention).
+
+## Verification Evidence
+
+| # | Command | Exit Code | Verdict | Duration |
+|---|---------|-----------|---------|----------|
+| 1 | `ssh ub01 'docker exec chrysopedia-api python3 /app/scripts/reindex_lightrag.py --dry-run --limit 3'` | 0 | ✅ pass | 3200ms |
+| 2 | `ssh ub01 'curl -sf http://localhost:9621/documents/status_counts'` | 0 | ✅ pass (processed: 4→6, all: 8) | 2700ms |
+| 3 | `ssh ub01 'docker ps --filter name=chrysopedia --format ...'` | 0 | ✅ pass (all healthy) | 3400ms |
+| 4 | `ssh ub01 'curl -sf http://localhost:9621/graph/label/list'` | 0 | ✅ pass (168 entities) | 3400ms |
+| 5 | `ssh ub01 'curl -sf --max-time 60 -X POST http://localhost:9621/query ...'` | 28 | ⏳ timeout (LLM busy with indexing) | 60000ms |
+
+
+## Deviations
+
+None.
+
+## Known Issues
+
+Query endpoint times out during active indexing due to shared LLM backend. Full reindex takes 3-6 hours for all 90 pages.
+
+## Files Created/Modified
+
+- `backend/scripts/reindex_lightrag.py`
+
+
+## Deviations
+None.
+
+## Known Issues
+Query endpoint times out during active indexing due to shared LLM backend. Full reindex takes 3-6 hours for all 90 pages.