Second audit axis (data, not code): is the information in the DB actually good?
Baseline scan of the live 29-paper corpus + four open investigation items
prepared self-contained for a cold session.
- Good: chunks 0/1507 fail the F-16 re-gate, healthy sizing, 0 dups.
- DQ-1 (HIGH): 12/29 papers have zero citations; 11 of them have an openalex_id,
so OpenAlex returned empty referenced_works (source-coverage limit, not a bug)
— propose an S2 references supplement.
- DQ-2 (MED): 3 papers no abstract; 1911.00966 fully metadata-less (OpenAlex 404).
- DQ-3 (MED): chunk-vs-source fidelity not yet verified.
- DQ-4 (MED): retrieval relevance not yet measured.
Includes connection steps, exact ids, priorities, and a reproduce appendix.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Re-ran the citation graph after the C-7 re-ingest (29/29 papers canonical/bare):
489 nodes, 590 edges, 472 dangling, 5.4% spread. The resolution fix's signature:
Pinkall/Polthier 1993 resolves to its DOI and is now the rank-1 *in-KB* hub
(was a dangling OpenAlex node); Bobenko/Springborn 2007 holds rank 7. Foundational
hubs still surface — GO re-affirmed on the shipping topology. Updates the ADR
spike table with before/after numbers.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The C-7 re-ingest hit M-1 live: TRUNCATE succeeded, then ingest failed on the
missing chunks.section column (schema.sql never applied to the live DB). Adding
the column then failed with 'must be owner' — the app user 'researcher' has DML
+ TRUNCATE but not DDL on the postgres-owned core tables. M-1's fix therefore
needs a privileged migration role, not just an idempotent schema. Records the
unblock and the helper's new preflight.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The ADR's GO rested on a live-corpus spike (478 dangling, Bobenko/Springborn
rank 7, 5.7% spread) measured before the resolution + canonicalisation landed.
Add an audit addendum: mark the 'Known Limitation: ID-Format Mismatch' as
resolved (C-1 shared resolver + C-7 canonical ids), and flag the Spike Result
numbers as pending re-measurement after the C-7 re-ingest. History preserved.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- Part D synthesis: C-11 HIGH (lead-ID collision → silent overwrite), R-8 MED, D-4 LOW.
- Part E wiki-rest: R-9 MED (cross-ref injection corrupts LaTeX math), C-12/C-13/R-10/R-11 LOW.
- Part F embed/quality/models: C-14/R-12 LOW + C-7 corroboration. Cleanest modules.
- Part G cli/config: C-15 MED (embedding_dim vs hardcoded vector(1024)), R-13/S-4/R-14/D-5 LOW.
Executive summary: 45 findings total (8 HIGH, 11 MED, 26 LOW). Five root themes;
dominant one is un-normalized identity (C-1/C-7/C-10/M-1). Whole repo reviewed.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Closes request (a) — the second pass over loop-1 §8 open items:
- Part A grounding guard: C-4 (HIGH, zero-claim pages bypass quarantine),
C-5/R-1 MED, C-6/R-2/R-3 LOW.
- Part B sources/: C-7 (HIGH, papers.id stored in OpenAlex URL form vs the
bare-ID contract), T-3 MED, R-4/R-5/C-9 LOW.
- Part C parsing/: C-10 MED (formulas/figures key on filename not paper.id),
R-6/R-7 LOW — all latent (live corpus is .txt).
Running tally: 30 findings, 7 HIGH. Common root: un-normalized identity.
Parts D-G (synthesis/wiki/embed/cli) still open.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Audit of main @5dfa6e4: 4 HIGH (S-1 secret-in-tree, M-1 missing migration
path, C-1 unpropagated ID-mismatch fix in discover.py, D-1 stale ADR-F15
validation, T-1 untested resolution SQL) plus MED/LOW findings. Findings
only; remediation planning deferred to the next loop phase.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Closes audit N-02: docs/adr/ADR-F13-synthesis-engine.md was missing,
blocking R-34. Documents spike result (GO, Opus APPROVE 2 passes),
four-stage lead taxonomy, grounding discipline, three-level
zero-fact-leak invariant, and falsification-gate in _parse_conjecture_output.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
