Forgejo categorically blocks --force-with-lease on protected branches,
even for fast-forward pushes. The cherry-picked branch is already a
descendant of origin/main, so a regular push is a fast-forward by
definition. Non-ff is rejected by default — same safety guarantee.
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>
The skip loop only matched `- ` (no indent) but YAML list items are
commonly written as ` - item` (2-space indent). This caused old list
items to persist alongside new ones, corrupting frontmatter on merge.
Fix: consume any line starting with space or dash as part of the current
field's value block.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Combined superset assertion and merge computation into single loop
(removed duplicate scalar-to-list normalization)
- Added worktree remove --force before worktree add to handle prior
crash leaving stale worktree (SIGKILL, OOM, power loss)
Two fixes from Ganymede review:
1. CRITICAL: blank line before closing --- compounded on repeat reweaves.
Body starts with \n---, so \n{body} created \n\n---. Fixed by checking
body prefix.
2. Replaced yaml.dump round-trip with _serialize_edge_fields() that splices
only edge arrays into raw frontmatter text. Non-edge fields (title,
confidence, type, quotes, flow styles) stay byte-identical to main HEAD.
_parse_yaml_frontmatter now returns 3-tuple: (dict, raw_fm_text, body).
_serialize_frontmatter takes (raw_fm_text, merged_edges_dict, body).
26 tests pass including idempotency (5x serialize), formatting preservation,
and no-blank-line regression test.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Reweave PRs modify existing files (appending YAML edges). Cherry-pick
fails ~75% when main moves between PR creation and merge.
_merge_reweave_pr() reads each changed file from both main HEAD and
branch HEAD, unions the edge arrays (order-preserving, main-first),
and writes the result. Eliminates merge conflicts structurally.
Key design decisions (Ganymede + Theseus approved):
- Order-preserving dedup: main's edges first, branch-new appended
- Superset assertion: logs warning if branch missing main edges
- Uses main's body text (reweave only touches frontmatter)
- Loud failure on parse errors (no cherry-pick fallback)
- Append-only contract: reweave adds edges, never removes
18 tests covering parse, union, serialize, superset, and full workflow.
_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>
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>
- 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>
