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>
Each stage (find_connections/gaps/improvements/propose_conjectures) numbered its
leads from seq=1, so connection L-0001, gap L-0001 and improvement L-0001 all
resolved to grounded/L-0001.md. The CLI concatenates them
(connections + gaps + improvements) and write_leads writes in order, so later
kinds silently overwrote earlier ones — survivors = max(per-kind count), not the
sum. Reproduced: 4 distinct leads -> 2 files.
_make_lead_id now takes the kind and emits L-C-/L-G-/L-I-/L-X- prefixes, keeping
same-seq ids distinct across stages. Regression tests cover the format and the
no-collision invariant.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Committed code predated the line-length=100 ruff config; this brings the
five drifted files into compliance. No logic change.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- Lead.__post_init__: raises ValueError on empty provenance list
- find_gaps: no-chunk path now carries topic-marker Provenance instead of []
- _update_index: docstring corrected (rebuilds, not append-only)
- test_model: test_lead_empty_provenance_raises covers the new invariant
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
