merge: R-C (.tex ingest) + R-F (section labels) + DQ-5 arXiv fix

docs/audit/DATA-QUALITY-2026-06-15.md

@@ -396,7 +396,33 @@ is self-contained so a cold session can pick it up.
 - **Acceptance:** Crossref recovers refs and/or an abstract for ≥1 paper where
   OpenAlex+S2 are empty.
 
-### R-C — Prefer arXiv `.tex` source over `.txt` for chunk fidelity · **MED lever, MED-HIGH effort**
+### R-C — Prefer arXiv `.tex` source over `.txt` for chunk fidelity · **DONE 2026-06-17**
+
+**Resolution (what was done) — all 13 arXiv papers re-ingested from `.tex`:**
+- **Multi-file flatten:** `arxiv.fetch_source` now inlines `\input`/`\include`
+  (`tex.flatten_inputs`) so multi-file projects yield the full body, not the
+  primary file's include skeleton (e.g. math/0603097 = 15 files / 12 includes;
+  2305.10988 = 6 / 5). Also handles legacy single-file **bare-gzipped** `.tex`
+  (no tar wrapper) for old math/* papers (commit 121b582).
+- **Section-aware chunking:** new `tex.chunk_sections` returns `(title, chunk)`
+  pairs (chunks never span a `\section`); the ingest `.tex` path labels the stored
+  `section` from the real heading instead of running `classify_section` on a
+  header-less word-window. Quality-gated as pairs so labels stay aligned.
+- **Unblocked by the arXiv half of DQ-5** (commit f504ca6): `_canonical_id`
+  strips the `10.48550/arxiv.` DOI prefix so an arXiv paper's id is the bare
+  arXiv id — without it, re-ingest tripped `papers_openalex_id_key` (confirmed
+  live, then fixed; idempotent re-ingest verified).
+- **Outcome:** `section` column gained signal — ~34/329 arXiv chunks now
+  intro/theorem/proof (was ~all `body`); math/0603097 `{body:31}`→`{body:29,
+  proof:9}`, 2310.17529 gained proof+intro, etc. Math papers with descriptively
+  titled sections stay `body` (classify_section's fixed vocab) — modest but real
+  (R-12). No paper gutted (chunk counts stable/▲); F-16 gate unchanged.
+- **Files:** `codex/parsing/tex.py`, `codex/sources/arxiv.py`, `codex/ingest.py`,
+  `codex/sources/openalex.py`, `scripts/rc_tex_reingest.py` (driver, dry-run
+  default), + tests. Full suite **370 passed**; ruff/mypy clean. Branch
+  `feat/tex-ingest` (commits 1da81c7, 121b582, f504ca6).
+
+**Original plan (for context):**
 - **What:** re-ingest from arXiv LaTeX source through the existing
   `codex.parsing.tex.latex_to_text` path instead of flattened `.txt`.
 - **Why:** highest-fidelity input — preserves math, structure, and section
@@ -428,6 +454,32 @@ is self-contained so a cold session can pick it up.
   violates most publisher terms and can get the whole institution's access
   revoked.** Do not wire a publisher login into the ingest pipeline.
 
+### R-F — Richer section labels: store real `\section` titles · **DONE 2026-06-17**
+
+**Resolution (what was done):**
+- **Why:** R-C labelled `.tex` chunks by mapping the real `\section` heading through
+  `classify_section`'s fixed vocab, so descriptively-titled Math sections collapsed
+  to `body` (only **34/329 = 10 %** non-`body`). A research pass confirmed the
+  `section` column is **write-only** (nothing filters on the vocab — `mcp_server.py`
+  and `wiki.py` don't even SELECT it), so storing free-text titles is safe.
+- **Change:** new `quality.section_label(title, content)` (+ `_clean_title`) — keep the
+  controlled bucket (intro/theorem/proof/abstract/bibliography) when the heading maps
+  to one, else store the cleaned real title ("the flip algorithm", "main results", …).
+  The `.tex` ingest path uses it; `.pdf`/`.txt`/`run_quality_pass` keep
+  `classify_section` unchanged. `_clean_title` strips LaTeX commands/accents/ties +
+  leading numbering, lower-cases, truncates at a word boundary. ~1 helper + 1 ingest
+  line; no schema change (column already free `TEXT`).
+- **Result (live):** re-applied to the 13 arXiv papers → non-`body` **34/329 (10 %) →
+  314/329 (95 %)**. Only `math/0306167` (old AMS-TeX, no `\section{}`) stays `body`.
+- **Tests:** `section_label` / `_clean_title` units + `.tex` ingest stores a
+  descriptive heading verbatim. Full suite 377 passed; ruff/mypy clean. Branch
+  `feat/section-labels` (off `feat/tex-ingest`).
+- **Accent re-clean — DONE 2026-06-17.** The `_clean_title` polish (`m\"obius`→`mobius`,
+  `~` ties, word-boundary truncation) landed in code, and the existing live labels were
+  re-cleaned in place (apply `_clean_title` to any `chunks.section` containing `\` or
+  `~`; **8 labels** fixed, no re-embed). Verified: **0** labels with LaTeX artifacts
+  remain; non-`body` holds at **314/329 (95 %)**. R-F fully complete.
+
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 ## Priority for the next session