feat(tex): section-aware multi-file .tex ingest (R-C)

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>

scripts/rc_tex_reingest.py

@@ -0,0 +1,125 @@
+"""R-C — re-ingest arXiv papers from LaTeX source (section-aware, higher fidelity).
+
+For each arXiv paper, download its source via :func:`codex.sources.arxiv.fetch_source`
+(multi-file ``\\input``/``\\include`` flattened), write it to a temp ``.tex``, and
+re-ingest through :func:`codex.ingest.ingest_paper`. The ``.tex`` ingest path is
+section-aware (:func:`codex.parsing.tex.chunk_sections`), so the stored ``section``
+column is labelled from real ``\\section`` headings instead of mostly ``body`` —
+serving DQ-3 (fidelity vs the OCR'd ``.txt``) and audit R-12 (weak ``section`` column).
+
+Only arXiv papers have downloadable source; DOI/journal papers and books are skipped.
+Re-ingest REPLACES the paper's chunks (DELETE + re-INSERT) — that is the intended R-C
+improvement (flattened ``.txt`` → clean ``.tex`` chunks). It is idempotent and
+**dry-run by default**; pass ``--write`` to mutate the live corpus.
+
+Usage
+-----
+    # dry-run: list arXiv papers + source availability (no writes)
+    PYTHONPATH=. python scripts/rc_tex_reingest.py
+
+    # re-ingest every arXiv paper from .tex
+    PYTHONPATH=. python scripts/rc_tex_reingest.py --write
+
+    # one paper
+    PYTHONPATH=. python scripts/rc_tex_reingest.py --only 2305.10988 --write
+
+Needs ``DATABASE_URL`` (Jetson tunnel) as documented in
+``docs/audit/DATA-QUALITY-2026-06-15.md``.
+"""
+
+from __future__ import annotations
+
+import argparse
+import logging
+import tempfile
+
+import psycopg
+import psycopg.rows
+
+from codex.db import get_conn
+from codex.ingest import ingest_paper
+from codex.sources import arxiv
+
+logger = logging.getLogger(__name__)
+
+
+def is_arxiv_id(paper_id: str) -> bool:
+    """Return True for arXiv ids (the only papers with downloadable LaTeX source).
+
+    arXiv ids are modern (``2305.10988``) or legacy (``math/0603097``). DOIs start
+    with ``10.``; OpenAlex W-ids start with ``W`` or an ``https://openalex.org/`` URL.
+    """
+    p = (paper_id or "").strip()
+    return bool(p) and not p.startswith("10.") and not p.startswith(("W", "https://"))
+
+
+def _section_dist(conn: psycopg.Connection[psycopg.rows.DictRow], paper_id: str) -> dict[str, int]:
+    """Return the section-label distribution for a paper's stored chunks."""
+    rows = conn.execute(
+        "SELECT coalesce(section, '(null)') AS s, count(*) AS n "
+        "FROM chunks WHERE paper_id = %s GROUP BY 1 ORDER BY 2 DESC",
+        (paper_id,),
+    ).fetchall()
+    return {r["s"]: int(r["n"]) for r in rows}
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--only", default=None, help="restrict to a single arXiv id")
+    parser.add_argument("--limit", type=int, default=None, help="cap number of papers")
+    parser.add_argument(
+        "--write", action="store_true", help="re-ingest into the live DB (default: dry-run)"
+    )
+    args = parser.parse_args(argv)
+    logging.basicConfig(level=logging.INFO, format="%(levelname)s %(message)s")
+
+    with get_conn() as conn:
+        rows = conn.execute("SELECT id FROM papers ORDER BY id").fetchall()
+    targets = [
+        r["id"]
+        for r in rows
+        if is_arxiv_id(r["id"]) and (args.only is None or r["id"] == args.only)
+    ]
+    if args.limit is not None:
+        targets = targets[: args.limit]
+
+    logger.info(
+        "arXiv papers to process=%d | mode=%s",
+        len(targets),
+        "WRITE" if args.write else "DRY-RUN",
+    )
+
+    for pid in targets:
+        try:
+            src = arxiv.fetch_source(pid)
+        except Exception as exc:
+            logger.warning("%s: source fetch failed: %s", pid, exc)
+            continue
+        if not src:
+            logger.warning("%s: no LaTeX source available — skipping", pid)
+            continue
+        if not args.write:
+            logger.info("%s: source OK (%d chars)", pid, len(src))
+            continue
+
+        with get_conn() as conn:
+            before = _section_dist(conn, pid)
+        with tempfile.NamedTemporaryFile("w", suffix=".tex", delete=True) as tf:
+            tf.write(src)
+            tf.flush()
+            res = ingest_paper(pid, source_path=tf.name)
+        with get_conn() as conn:
+            after = _section_dist(conn, pid)
+        logger.info(
+            "%s: chunks %d->%d | section before=%s after=%s",
+            pid,
+            sum(before.values()),
+            res.chunks_upserted,
+            before,
+            after,
+        )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())