Root cause of 84% reweave PR rejection rate: claim titles with colons
(e.g., "COAL: Meta-PoW: The ORE Treasury Protocol") written as bare
YAML list items, causing yaml.safe_load to fail during merge.
Three changes:
1. frontmatter.py: _yaml_quote() wraps colon-containing values in double quotes
2. reweave.py: _write_edge_regex uses _yaml_quote for new edges
3. merge.py: skip individual files with parse failures instead of aborting entire PR
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Orphan ratio at 39.6% (443/1118 claims) vs <15% target. Root cause:
reweave threshold 0.70 too strict for text-embedding-3-small — 56% of
orphans found "no neighbors." At 0.55, dry-run shows 0% no-neighbor
skips. Batch size 200 clears backlog in ~3-4 nights at ~$0.20/run.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Three fixes from Ganymede's review of extract-time-connection:
1. Replace git add -A with explicit file staging in _reciprocal_edges
2. Push to origin/main immediately after commit (survive batch-extract reset)
3. RECIPROCAL_EDGE_MAP: challenges→challenged_by (not symmetric)
Added challenged_by to REWEAVE_EDGE_FIELDS, EDGE_FIELDS, EDGE_WEIGHTS
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Also fixes _is_entity path check to use Path.parts instead of string
containment, preventing false positives on paths like "domains/entities-overview/".
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Atomic extract-and-connect (lib/connect.py):
- After extraction writes claim files, each new claim is embedded via
OpenRouter, searched against Qdrant, and top-5 neighbors (cosine > 0.55)
are added as `related` edges in the claim's frontmatter
- Edges written on NEW claim only — avoids merge conflicts
- Cross-domain connections enabled, non-fatal on Qdrant failure
- Wired into openrouter-extract-v2.py post-extraction step
Stale PR monitor (lib/stale_pr.py):
- Every watchdog cycle checks open extract/* PRs
- If open >30 min AND 0 claim files → auto-close with comment
- After 2 stale closures → marks source as extraction_failed
- Wired into watchdog.py as check #6
Response audit system:
- response_audit table (migration v8), persistent audit conn in bot.py
- 90-day retention cleanup, tool_calls JSON column
- Confidence tag stripping, systemd ReadWritePaths for pipeline.db
Supporting infrastructure:
- reweave.py: nightly edge reconnection for orphan claims
- reconcile-sources.py: source status reconciliation
- backfill-domains.py: domain classification backfill
- ops/reconcile-source-status.sh: operational reconciliation script
- Attribution improvements, post-extract enrichments, merge improvements
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
