1. Remove hardcoded [[_map]] dead link from reconstruct_claim_content
2. Add source status check + archive move after extraction (prevents re-extraction loops)
3. Fix wiki link slug→space normalization (resolves hyphens to spaces before stripping)
Pentagon-Agent: Epimetheus <0144398e-4ed3-4fe2-95a3-3d72e1abf887>
_retry_conflict_prs called _rebase_and_push which was never defined,
causing NameError on every conflict retry. Now uses _cherry_pick_onto_main
consistent with the primary merge path.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Layer 1: Insertion-time dedup in openrouter-extract-v2.py — skip if source_slug
already appears in claim content.
Layer 2: Insertion-time dedup in entity_batch.py — skip if PR number already
enriched this claim.
Layer 3: Post-rebase dedup in merge.py — scan rebased files for duplicate
evidence blocks (same source reference) and remove them before force-push.
Root cause: multiple enrichment branches modify the same claim at the same
insertion point. When rebased sequentially, evidence blocks are duplicated.
(Leo: PRs #1751, #1752)
lib/dedup.py: standalone module — parses evidence headers, deduplicates by
source key, preserves trailing content (Relevant Notes, Topics sections).
9 tests covering all patterns including the real PR #1751 duplication case.
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>
Gate 3 in batch-extract-50.sh: query pipeline.db for closed PRs before
re-extracting. Sources with >=3 closed PRs are skipped (zombie protection).
Cost tracking: openrouter_call() now returns (text, usage) tuple with
prompt_tokens and completion_tokens from the OpenRouter API response.
All callers updated to unpack and pass tokens to costs.record_usage().
Added missing triage cost recording. Fixed batch domain review recording
cost once per batch instead of once per PR.
Pentagon-Agent: Epimetheus <0144398e-4ed3-4fe2-95a3-3d72e1abf887>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
After a PR merges successfully, _embed_merged_claims() diffs the merged SHA
against its parent to find new/changed .md files in knowledge directories
(domains/, core/, foundations/, decisions/, entities/). Each file is embedded
via embed-claims.py --file (OpenRouter, text-embedding-3-small).
Non-fatal: embedding failure logs a warning but does not block the merge
pipeline. This keeps vector search current without requiring manual re-embeds.
Pentagon-Agent: Epimetheus <3D35839A-7722-4740-B93D-51157F7D5E70>
Root cause of 5-day pipeline stall: fixer GC marked PRs as closed in DB
but never synced to Forgejo. Branches stayed alive on remote, blocking
Gate 2 in batch-extract (branch exists → skip forever).
Now: GC fetches PR numbers, posts audit comment, closes on Forgejo,
deletes remote branch, THEN updates DB. Same pattern as _terminate_pr
in evaluate.py.
Pentagon-Agent: Epimetheus <3D35839A-7722-4740-B93D-51157F7D5E70>
- Claim-shape detector: if YAML has type: claim, force STANDARD minimum (Theseus)
- Random pre-merge promotion: 15% of LIGHT → STANDARD before eval (Rio)
- LIGHT_SKIP_LLM config flag: skip domain+Leo review for LIGHT (Rhea: env var rollback)
- Updated both_approve: domain_verdict=skipped is valid for LIGHT auto-approve
- Cost recording: only charge for reviews that actually ran
- SAMPLE_AUDIT_RATE bumped 0.10 → 0.15, audit model = Opus (Leo: different family from Haiku)
Multi-agent design review: Rio (gaming vectors, model diversity), Theseus (correlated
blindspots, claim-shape guard), Rhea (shadow mode, config flag, deployment), Leo (approval).
Pentagon-Agent: Ganymede <F99EBFA6-547B-4096-BEEA-1D59C3E4028A>
Forgejo returns 200 with HTML content-type on successful merge instead
of JSON. Our API helper threw on resp.json(), causing merge to report
failure even though the PR merged. Now treats non-JSON 200 as success.
This was causing PRs #732 and #789 to show as conflict in our DB while
actually merged on Forgejo, and tripping the merge circuit breaker.
Pentagon-Agent: Leo <294C3CA1-0205-4668-82FA-B984D54F48AD>
Unevaluated PRs (eval_attempts=0) now sort before re-evals in the
eval cycle query. Fresh PRs have a higher chance of passing (~12%)
vs re-evals of already-rejected PRs. Prevents migration-reset PRs
from consuming eval slots that fresh PRs could use.
Pentagon-Agent: Leo <294C3CA1-0205-4668-82FA-B984D54F48AD>
Opus was ignoring the valid tag list and generating custom tags like
schema-enrichment-slug-mismatch, which fall through to 'unknown' in
disposition logic. All three prompts (domain, Leo standard, Leo deep)
now explicitly say "do not invent new tags" alongside the valid tag list.
Pentagon-Agent: Leo <294C3CA1-0205-4668-82FA-B984D54F48AD>
If source_path is NULL, the source requeue silently matches nothing.
Log a warning so we catch orphaned terminations in monitoring.
Pentagon-Agent: Leo <294C3CA1-0205-4668-82FA-B984D54F48AD>
Schema migration v3: adds eval_attempts (INTEGER) and eval_issues (TEXT/JSON)
columns to prs table.
Retry budget logic (Ganymede-approved design):
- Increment eval_attempts on each evaluate_pr() call
- Hard cap: eval_attempts >= 3 → terminal (close PR, tag source needs_human)
- Attempt 1: normal — back to open, wait for fix
- Attempt 2: classify issues as mechanical/substantive
- Mechanical only (schema, wiki links, dedup): keep open for one more try
- Substantive (factual, confidence, scope, title): close PR, requeue source
- Issue tags parsed from reviewer comments, stored in eval_issues column
- SHA-based reset: new commits on PR branch → eval_attempts=0, verdicts reset
- Post-migration stagger: LIMIT 5 for first batch to avoid OpenRouter spike
- Cost recording updated: domain review → OpenRouter, Leo → tier-dependent
Stops the 32-PR infinite loop burning ~$0.03/cycle with no terminal state.
Pentagon-Agent: Leo <294C3CA1-0205-4668-82FA-B984D54F48AD>
- Domain review → GPT-4o (OpenRouter), Leo STANDARD → Sonnet (OpenRouter),
Leo DEEP → Opus (Claude Max). Two model families = no correlated blind spots.
- Opus reserved for DEEP eval only — protects rate limit for overnight research.
- Review prompts calibrated: require per-criterion evidence, blocking-vs-observation
verdict rules. Moved from 100% rubber-stamp approval to 12% pass rate.
- OpenRouter failures classified as openrouter_failed (not rate_limited) to avoid
spurious 15-min Opus backoff.
- merge.py: pre-check PR state before merge API call (prevents 405 on re-merge).
Pentagon-Agent: Leo <294C3CA1-0205-4668-82FA-B984D54F48AD>
- Fix#12: domain_review undefined on resume path — initialize to None,
guard _parse_issues() call. Prevents NameError on PRs resuming after
partial eval (76 PRs in this state right now).
- Fix#11: concurrent eval workers can duplicate reviews — add atomic
UPDATE SET status='reviewing' WHERE status='open' at top of
evaluate_pr(). Check rowcount, skip if already claimed.
- Fix#8: subprocess tracking for graceful shutdown — _active_subprocesses
set in evaluate module, tracked in _claude_cli_call, exposed via
kill_active_subprocesses(). Replaces dead code in teleo-pipeline.py.
- Fix health.py divide-by-zero — guard all metabolic metric reads against
None from NULLIF/empty result set. Prevents TypeError on /health when
no PRs have been evaluated in 24h.
Also includes Leo's existing hot-fixes:
- Rate limit detection checks stdout regardless of exit code
- 15-minute cycle-level backoff on rate limit
Pentagon-Agent: Ganymede <F99EBFA6-547B-4096-BEEA-1D59C3E4028A>
