Resolved 4 conflicts: cli.py (R-D citing-coverage warning + main's small-corpus JSON/hub-title changes both kept); ingest.py (C-7 paper.id=caller-id pin first, then DQ-2 abstract recovery); test_ingest.py + test_openalex.py (kept both branches' tests).
C-7/DQ-5 overlap (both canonicalise papers.id): kept both layers — openalex._canonical_id normalizes fetch_paper's id (DQ-5); ingest pins papers.id to the caller's bare id (C-7); they converge on the bare canonical id. Fixed the auto-merged test_fetch_paper_success that had contradictory bare/URL assertions. 402 tests pass; ruff + mypy clean.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Flatten multi-file arXiv LaTeX (\input/\include) in arxiv.fetch_source so the full body is assembled rather than just the primary file's include skeleton, and add section-aware chunking (tex.chunk_sections) so .tex chunks never span a \section boundary and are labelled by their real heading. The ingest .tex path now produces (section, chunk) pairs, quality-gated together so labels stay aligned; the stored 'section' column gains genuine signal instead of mostly 'body' (serves DQ-3 fidelity + audit R-12).
Adds scripts/rc_tex_reingest.py to re-ingest arXiv papers from .tex (dry-run by default; replaces chunks). Tests: flatten_inputs, chunk_sections, multi-file fetch_source, section-label ingest, is_arxiv_id. Full suite 365 passed; ruff + mypy clean.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
database_url, migration_database_url, mcp_auth_token and the mathpix app
id/key are now pydantic SecretStr, so they render as '**********' in any
repr/log/traceback instead of leaking the plaintext credential. Consumers
(db.get_conn, cli.migrate, mcp._require_http_token, mathpix.extract_formulas)
call .get_secret_value() at the point of use. Tests updated to the SecretStr
type.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Review-Gate finding: GROBID emits type="arXiv" (camel-case), not "arxiv".
XPath literal match silently returned empty strings for all real responses.
Fix: iterate idno elements and compare .lower() == "arxiv".
Test fixture updated to reflect real GROBID output (type="arXiv").
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
