- D-2 config.py: graph_cite_boost_alpha described the OLD inverted formula
(score = dense * (1 + alpha*pr)); the code divides distance. Document the
actual boosted_distance = distance / (1 + alpha*pr).
- D-4 synthesis.py: write_leads claimed an 'append-only' INDEX.md that keeps
previously-recorded ids; _update_index actually rebuilds from on-disk glob.
Docstring now matches the implementation.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
discover.py compared the raw OpenAlex cited_id against papers.id (a DOI/arXiv
id), so an ingested paper cited by its OpenAlex id was mis-reported as a
discovery lead. graph.py already resolved this via papers.openalex_id, but the
fix was never propagated — two 'dangling' implementations disagreed.
Extract the resolution into one shared constant RESOLVED_CITATIONS_SQL in
graph.py; build_citation_graph and all four discover.py queries
(discovery_leads / citing_papers / cited_by / cocited_papers) now go through it,
so the 'what counts as ingested' rule cannot drift again.
Live-DB validated: before, 13 ingested papers leaked into discovery_leads;
after, the real discovery_leads() returns 0 ingested papers among its leads.
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>
compile_all's quarantine gate was guarded by `total_claims > 0`, so a page
with no parseable citations — including the LLM-outage case where
compile_concept returns an empty page — fell through to the publish branch and
was written to wiki/ + marked compiled. Such a page carries zero grounding
evidence.
Now: total_claims == 0 (or grounding_rate below threshold) quarantines and does
NOT update the compile-state, so a transient LLM failure retries next run
instead of freezing an empty/uncited page as 'compiled'. Empty bodies are
recorded but not written as draft files.
Regression test reproduces the exact bypass (uncited LLM output -> quarantined,
not published).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
