Tarik Moussa c4106b0f51 fix(synthesis): make coverage-map gaps opt-in (audit R-8) ...

find_gaps defaulted its probe topics to paper titles, so a title — which
retrieves mostly its own single bibkey — fell below synthesis_gap_min_coverage
and flagged almost every paper as a 'gap'. Coverage-map gaps now run only for
explicitly-requested topics; the CLI gains a repeatable --topic option. The
code-vs-corpus gap path (precise) is unchanged and still default.

Tests: the two cases that relied on default-title coverage gaps now pass explicit
topics; added a regression that no coverage gaps appear without --topic.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

2026-06-15 16:32:01 +02:00

..

parsing

fix(F-09): address review-gate findings — resource leak + idempotency

2026-06-14 02:23:21 +02:00

sources

style: ruff format normalization to line-length=100

2026-06-15 08:43:53 +02:00

__init__.py

feat: initial project scaffold

2026-06-04 11:19:10 +02:00

__main__.py

fix(ingest): D-04 bibkey heuristic + D-05a/b/c regression tests + __main__

2026-06-15 03:07:06 +02:00

cli.py

fix(synthesis): make coverage-map gaps opt-in (audit R-8)

2026-06-15 16:32:01 +02:00

config.py

feat(db): idempotent schema + 'codex migrate' command (audit M-1, T-2)

2026-06-15 15:53:25 +02:00

db.py

feat(db): idempotent schema + 'codex migrate' command (audit M-1, T-2)

2026-06-15 15:53:25 +02:00

discover.py

fix(discover): resolve cited_id via shared resolver (audit C-1)

2026-06-15 11:12:55 +02:00

embed.py

feat(embed): BGE-M3 dense+sparse via FlagEmbedding (ADR-0002)

2026-06-04 23:48:06 +02:00

graph.py

fix(discover): resolve cited_id via shared resolver (audit C-1)

2026-06-15 11:12:55 +02:00

ingest.py

fix(ingest): key formulas/figures on papers.id, not filename stem (audit C-10)

2026-06-15 12:09:38 +02:00

mcp_server.py

fix(mcp): disable DNS rebinding protection for LAN HTTP transport

2026-06-14 14:55:29 +02:00

models.py

feat(F-09): rich parsing — formula + figure extraction

2026-06-14 01:16:24 +02:00

provenance.py

feat(discover,provenance): graph discovery queries + @cite scan + code_links + bib export

2026-06-05 07:13:01 +02:00

quality.py

feat(F-16): chunk quality gate + section classification

2026-06-15 01:22:44 +00:00

synthesis.py

fix(synthesis): make coverage-map gaps opt-in (audit R-8)

2026-06-15 16:32:01 +02:00

wiki.py

fix(wiki): protect math in cross-refs; drop no-op DB call; fix mark order

2026-06-15 16:24:22 +02:00