.gitignore

@@ -38,3 +38,6 @@ htmlcov/
 
 # Claude Code — settings.json IS committed (team-wide); only personal overrides ignored
 .claude/settings.local.json
+
+# Generated wiki index (regenerated by `codex wiki compile`; concepts.yaml is the source)
+wiki/index.md

codex/cli.py

@@ -116,10 +116,10 @@ def search_paper(
         rows = conn.execute(
             """
             SELECT id, title, year,
-                   abstract_emb <-> %(emb)s AS distance
+                   abstract_emb <-> %(emb)s::vector AS distance
             FROM   papers
             WHERE  abstract_emb IS NOT NULL
-            ORDER  BY abstract_emb <-> %(emb)s
+            ORDER  BY abstract_emb <-> %(emb)s::vector
             LIMIT  %(limit)s
             """,
             {"emb": emb, "limit": limit},
@@ -596,7 +596,12 @@ def graph_report(
     """Show citation graph report: top hub papers, dangling citations, cluster summary."""
     from codex.config import get_settings
     from codex.db import get_conn
-    from codex.graph import build_citation_graph, citation_pagerank, dangling_citations
+    from codex.graph import (
+        build_citation_graph,
+        citation_pagerank,
+        citing_coverage,
+        dangling_citations,
+    )
 
     settings = get_settings()
     with get_conn() as conn:
@@ -613,6 +618,8 @@ def graph_report(
     pr = citation_pagerank(graph)
     hubs = sorted(pr.items(), key=lambda x: -x[1])[:top_n]
     dangling = sorted(dangling_citations(graph, known_ids))
+    n_citing, _ = citing_coverage(graph, known_ids)
+    coverage = n_citing / n_papers if n_papers else 0.0
     small_corpus = n_papers < settings.graph_min_corpus_size
     warning = (
         f"only {n_papers} ingested papers; recommended >= {settings.graph_min_corpus_size} "
@@ -627,6 +634,11 @@ def graph_report(
                 {
                     "nodes": graph.number_of_nodes(),
                     "edges": graph.number_of_edges(),
+                    "citing_coverage": {
+                        "citing": n_citing,
+                        "papers": n_papers,
+                        "fraction": round(coverage, 4),
+                    },
                     "small_corpus_warning": warning,  # null unless below threshold (audit U-3)
                     "hubs": [
                         {"paper_id": pid, "title": titles.get(pid), "pagerank": score}
@@ -642,7 +654,17 @@ def graph_report(
 
     if warning:
         typer.echo(f"Warning: {warning}.", err=True)
+    # R-D: low citing-paper coverage starves PageRank/coupling even at a healthy
+    # paper count — warn on the share of papers that actually have out-edges.
+    if coverage < settings.graph_min_citing_coverage:
+        typer.echo(
+            f"Warning: only {n_citing}/{n_papers} papers ({coverage:.0%}) have out-edges "
+            f"(recommended ≥ {settings.graph_min_citing_coverage:.0%}); "
+            f"low citing coverage weakens PageRank/coupling.",
+            err=True,
+        )
     typer.echo(f"Graph: {graph.number_of_nodes()} nodes, {graph.number_of_edges()} edges")
+    typer.echo(f"Citing coverage: {n_citing}/{n_papers} papers with out-edges ({coverage:.0%})")
     typer.echo("")
     typer.echo(f"TOP-{top_n} HUB PAPERS (PageRank)")
     typer.echo("-" * 48)

codex/config.py

@@ -322,6 +322,18 @@ class Settings(BaseSettings):
         ),
     )
 
+    graph_min_citing_coverage: float = Field(
+        default=0.8,
+        ge=0.0,
+        le=1.0,
+        description=(
+            "Minimum share of ingested papers that must have ≥1 out-edge (i.e. "
+            "cite something) before `codex graph report` warns. Low citing "
+            "coverage starves PageRank/coupling even when the paper count looks "
+            "healthy — the share of *citing* papers is what matters (R-D)."
+        ),
+    )
+
 
 @lru_cache(maxsize=1)
 def get_settings() -> Settings:

codex/graph.py

@@ -109,6 +109,20 @@ def citation_pagerank(graph: nx.DiGraph, *, damping: float = 0.85) -> dict[str,
     return cast(dict[str, float], nx.pagerank(graph, alpha=damping))
 
 
+def citing_coverage(graph: nx.DiGraph, known_ids: set[str]) -> tuple[int, int]:
+    """Return ``(papers_with_out_edges, total_papers)`` — the citing-paper coverage.
+
+    A paper "covers" the citation graph when it has ≥1 out-edge (it cites at least
+    one work). Low citing coverage starves the F-15 layer (PageRank / coupling /
+    co-citation) even when the total paper count looks healthy, because those
+    metrics are driven by out-edges, not by node count. Surfaced by
+    ``codex graph report`` (R-D); the warning threshold is
+    :attr:`codex.config.Settings.graph_min_citing_coverage`.
+    """
+    n_citing = sum(1 for pid in known_ids if pid in graph and graph.out_degree(pid) > 0)
+    return n_citing, len(known_ids)
+
+
 def find_related(paper_id: str, graph: nx.DiGraph, *, min_shared: int = 2) -> list[str]:
     """Bibliographic coupling: papers sharing ≥ ``min_shared`` references with ``paper_id``.
 

codex/ingest.py

@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-import contextlib
 import logging
 from dataclasses import dataclass
 from pathlib import Path
@@ -14,8 +13,8 @@ from codex.config import get_settings
 from codex.db import get_conn
 from codex.embed import get_embedder
 from codex.models import Citation, Paper
-from codex.quality import classify_section, filter_chunks
+from codex.quality import is_quality_chunk, section_label
-from codex.sources import openalex, semanticscholar
+from codex.sources import arxiv, crossref, openalex, semanticscholar
 
 logger = logging.getLogger(__name__)
 
@@ -48,6 +47,113 @@ def _make_bibkey(paper: Paper) -> str | None:
     return surnames[0] + "EtAl" + year
 
 
+def _s2_id_for(pid: str) -> str | None:
+    """Format a canonical paper id for the Semantic Scholar paper endpoint.
+
+    S2 needs a namespaced id (``arXiv:<id>``, ``DOI:<doi>``) or a bare 40-hex
+    S2 paperId — a bare arXiv id like ``2305.10988`` 404s. DOIs are detected by
+    the ``10.`` prefix; everything else is assumed to be an arXiv id (modern
+    ``2305.10988`` or legacy ``math/0603097``).
+    """
+    p = (pid or "").strip()
+    if not p:
+        return None
+    if p.lower().startswith(("arxiv:", "doi:")):
+        return p
+    if p.startswith("10."):
+        return f"DOI:{p}"
+    return f"arXiv:{p}"
+
+
+def _norm_cited_id(cited_id: str) -> str:
+    """Normalize a DOI cited-id to its canonical bare, lower-cased form.
+
+    DOIs are case-insensitive and may arrive bare (``10.…``), as a
+    ``https://doi.org/…`` URL, or ``doi:…``-prefixed: GROBID emits whichever
+    form the PDF reference text used, while S2/OpenAlex hand back bare DOIs.
+    Stripping the prefix and lower-casing keeps the citation-graph join from
+    fragmenting the same reference into distinct case-/URL-variant nodes. arXiv
+    ids and S2 paperIds are left untouched. Mirrors ``openalex._normalize_doi``."""
+    s = cited_id.strip()
+    lowered = s.lower()
+    for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):
+        if lowered.startswith(prefix):
+            return lowered[len(prefix) :]
+    return lowered if lowered.startswith("10.") else s
+
+
+def _recover_abstract(paper: Paper) -> str | None:
+    """Recover a missing abstract from S2, then Crossref (DQ-2 supplement).
+
+    Tried in order of coverage for this corpus: Semantic Scholar (indexes most
+    arXiv + journal abstracts), then Crossref (publisher-deposited, DOI only).
+    Network/parse failures degrade to None rather than aborting the ingest.
+    """
+    s2_id = _s2_id_for(paper.id)
+    if s2_id is not None:
+        try:
+            abstract = semanticscholar.fetch_abstract(s2_id)
+            if abstract and abstract.strip():
+                return abstract.strip()
+        except Exception:
+            logger.warning("S2 abstract recovery failed for %s", paper.id, exc_info=True)
+    if paper.id.startswith("10."):
+        try:
+            abstract = crossref.fetch_abstract(paper.id)
+            if abstract and abstract.strip():
+                return abstract.strip()
+        except Exception:
+            logger.warning("Crossref abstract recovery failed for %s", paper.id, exc_info=True)
+    return None
+
+
+def _s2_reference_supplement(paper: Paper) -> list[Citation]:
+    """Fetch a paper's references from Semantic Scholar (DQ-1 supplement).
+
+    Used when OpenAlex returns an empty ``referenced_works`` list — common for
+    arXiv preprints and institutional theses that OpenAlex indexes without a
+    parsed bibliography. ``citing_id`` is rewritten to the canonical ``paper.id``
+    so the FK holds, and cited DOIs are case-normalised. Network/parse failures
+    degrade to an empty list rather than aborting the ingest.
+    """
+    s2_id = _s2_id_for(paper.id)
+    if s2_id is None:
+        return []
+    try:
+        raw = semanticscholar.fetch_references(s2_id)
+    except Exception:
+        logger.warning("S2 reference supplement failed for %s", paper.id, exc_info=True)
+        return []
+    return [
+        Citation(citing_id=paper.id, cited_id=_norm_cited_id(c.cited_id), context=c.context)
+        for c in raw
+        if c.cited_id
+    ]
+
+
+def _crossref_reference_supplement(paper: Paper) -> list[Citation]:
+    """Fetch a paper's references from Crossref (roadmap R-B supplement).
+
+    Third leg of the citation fallback chain (OpenAlex-empty → S2 → Crossref).
+    Crossref carries publisher-deposited reference lists keyed on the citing
+    work's DOI, so only DOI papers can be looked up (arXiv-only ids → []).
+    ``citing_id`` is rewritten to the canonical ``paper.id`` and cited DOIs are
+    case-normalised. Network/parse failures degrade to [] rather than aborting.
+    """
+    if not paper.id.startswith("10."):
+        return []
+    try:
+        raw = crossref.fetch_references(paper.id)
+    except Exception:
+        logger.warning("Crossref reference supplement failed for %s", paper.id, exc_info=True)
+        return []
+    return [
+        Citation(citing_id=paper.id, cited_id=_norm_cited_id(c.cited_id), context=c.context)
+        for c in raw
+        if c.cited_id
+    ]
+
+
 def ingest_paper(
     paper_id: str,
     source_path: str | None = None,
@@ -89,10 +195,11 @@ def ingest_paper(
             len(paper_id) > 4 and paper_id[4:5] == "." and paper_id[:4].isdigit()
         )
         if looks_like_arxiv:
-            arxiv_key = paper_id if pid_lower.startswith("arxiv:") else f"arXiv:{paper_id}"
+            # OpenAlex 404 on an arXiv id → recover authoritative metadata from
-            with contextlib.suppress(Exception):
+            # the arXiv API (DQ-2); fall back to a minimal stub if arXiv also
-                semanticscholar.fetch_references(arxiv_key)
+            # has nothing. Citation recovery from S2 happens in the citation
-            paper = Paper(id=paper_id, title="")
+            # block below (DQ-1 supplement).
+            paper = arxiv.fetch_metadata(paper_id) or Paper(id=paper_id, title="")
         else:
             raise ValueError(f"Paper not found: {paper_id}")
 
@@ -100,12 +207,23 @@ def ingest_paper(
         raise ValueError(f"Paper not found: {paper_id}")
 
     # Canonical identity is the caller-supplied id — what the CLI / ingest scripts
-    # use and what papers.id is contracted to hold (arXiv id or DOI). OpenAlex's
+    # use and what papers.id is contracted to hold (arXiv id or DOI). Pin it to the
-    # fetch_paper fills paper.id with the URL-form doi/id (e.g.
+    # caller's id (audit C-7), but normalize it the same way cited-ids are (strip a
-    # "https://doi.org/10.48550/arxiv.math/0603097"), which broke bare-id lookups
+    # https://doi.org/ or doi: prefix, lower-case DOIs) so a non-bare caller cannot
-    # and cross-citation matching (audit C-7). The OpenAlex work id is retained
+    # store a URL-form papers.id that would defeat DQ-5's ON CONFLICT (id) idempotency
-    # separately as openalex_id and in the paper_identifiers alias table.
+    # or the `paper.id.startswith("10.")` recovery gates below. arXiv/W ids pass
-    paper.id = paper_id.strip()
+    # through unchanged. The OpenAlex work id is retained as openalex_id / in
+    # paper_identifiers.
+    paper.id = _norm_cited_id(paper_id.strip())
+
+    # DQ-2: OpenAlex often has the paper but no abstract (it cannot redistribute
+    # some publishers' abstracts). Supplement from S2, then Crossref (uses the
+    # canonical paper.id set above), so the paper gets a real (non-zero) abstract
+    # embedding instead of a zero vector.
+    if not (paper.abstract or "").strip():
+        recovered = _recover_abstract(paper)
+        if recovered:
+            paper.abstract = recovered
 
     # Auto-generate bibkey when source has none (D-04).
     if paper.bibkey is None:
@@ -208,44 +326,63 @@ def ingest_paper(
         if source_path is not None:
             from codex.parsing.grobid import extract_references
             from codex.parsing.nougat import pdf_to_markdown
-            from codex.parsing.tex import chunk_text, latex_to_text
+            from codex.parsing.tex import chunk_sections, chunk_text
 
             suffix = Path(source_path).suffix.lower()
-            text = ""
+            # (section_title | None, chunk_text) pairs. `.tex` is section-aware so
+            # the stored `section` column reflects the real heading (R-C / R-12);
+            # `.txt`/`.pdf` carry no section structure, so the title is None.
+            raw_pairs: list[tuple[str | None, str]] = []
 
             if suffix == ".tex":
-                text = latex_to_text(Path(source_path).read_text())
+                raw_pairs = chunk_sections(Path(source_path).read_text())
             elif suffix == ".txt":
                 text = Path(source_path).read_text(encoding="utf-8", errors="replace")
+                raw_pairs = [(None, c) for c in chunk_text(text)]
             elif suffix == ".pdf":
-                text = pdf_to_markdown(source_path)
+                raw_pairs = [(None, c) for c in chunk_text(pdf_to_markdown(source_path))]
                 # Also extract GROBID refs
                 grobid_refs = extract_references(source_path)
                 for ref in grobid_refs:
                     cited_id = ref.get("doi") or ref.get("arxiv_id")
                     if cited_id:
-                        pdf_citations.append(Citation(citing_id=paper.id, cited_id=cited_id))
+                        # Normalize the GROBID DOI (bare/URL/``doi:`` → bare lower-case)
+                        # so PDF-derived edges join the same graph nodes as the
+                        # S2/OpenAlex paths; arXiv ids pass through untouched.
+                        pdf_citations.append(
+                            Citation(citing_id=paper.id, cited_id=_norm_cited_id(cited_id))
+                        )
             else:
                 logger.warning("Unbekannter Dateityp: %s — kein Text-Parsing", source_path)
 
-            raw_chunks = chunk_text(text) if text else []
+            # Quality-gate the pairs (keeps each chunk aligned with its section title).
-            chunks_text = filter_chunks(raw_chunks, settings=get_settings())
+            settings = get_settings()
+            kept_pairs = [
+                (title, content)
+                for title, content in raw_pairs
+                if is_quality_chunk(content, settings=settings)
+            ]
 
             # Delete existing chunks for this paper
             conn.execute("DELETE FROM chunks WHERE paper_id = %s", (paper.id,))
 
-            if chunks_text:
+            if kept_pairs:
                 # Embed all chunks in one batch
-                chunk_embeddings = embedder.encode_dense(chunks_text)
+                chunk_contents = [content for _, content in kept_pairs]
+                chunk_embeddings = embedder.encode_dense(chunk_contents)
                 chunk_rows = [
                     (
                         paper.id,
                         ord_idx,
                         content,
                         chunk_embeddings[ord_idx].tolist(),
-                        classify_section(content),
+                        # .tex: label from the real \section heading — keeps the
+                        # controlled bucket when it matches, else stores the cleaned
+                        # title (R-F); .txt/.pdf (title=None) classify by content.
+                        # NB: `section` semantics now differ by source (write-only col).
+                        section_label(title, content),
                     )
-                    for ord_idx, content in enumerate(chunks_text)
+                    for ord_idx, (title, content) in enumerate(kept_pairs)
                 ]
                 with conn.cursor() as cur:
                     cur.executemany(
@@ -256,7 +393,7 @@ def ingest_paper(
                 chunks_upserted = len(chunk_rows)
 
         # ---------------------------------------------------------------
-        # 5. Fetch citations  (OpenAlex if openalex_id, else S2)
+        # 5. Fetch citations  (fallback chain: OpenAlex → S2 → Crossref)
         #    Insert with ON CONFLICT (citing_id, cited_id) DO NOTHING
         # ---------------------------------------------------------------
         api_citations: list[Citation]
@@ -267,8 +404,17 @@ def ingest_paper(
             api_citations = [
                 Citation(citing_id=paper.id, cited_id=c.cited_id, context=c.context) for c in raw
             ]
+            # DQ-1: OpenAlex indexes many arXiv preprints / theses WITHOUT a
+            # parsed reference list (referenced_works == []). Fall back to the
+            # Semantic Scholar references, which often has them.
+            if not api_citations:
+                api_citations = _s2_reference_supplement(paper)
         else:
-            api_citations = semanticscholar.fetch_references(paper_id)
+            api_citations = _s2_reference_supplement(paper)
+        # R-B: if OpenAlex and S2 both came back empty, try Crossref's
+        # publisher-deposited references (DOI papers only) as a third leg.
+        if not api_citations:
+            api_citations = _crossref_reference_supplement(paper)
 
         # Merge API citations and GROBID PDF citations; dedup via set
         all_citations_set: set[tuple[str, str]] = set()

codex/parsing/grobid.py

@@ -26,6 +26,7 @@ def _text(element: ET.Element | None) -> str:
 def extract_references(
     pdf_path: str,
     grobid_url: str | None = None,
+    timeout: float = 60.0,
 ) -> list[dict[str, str]]:
     """Extract a structured reference list from a PDF via GROBID.
 
@@ -35,6 +36,9 @@ def extract_references(
         Path to the PDF file on disk.
     grobid_url:
         Base URL of the GROBID server.  Defaults to ``Settings().grobid_url``.
+    timeout:
+        HTTP client timeout in seconds.  Large PDFs (e.g. theses) can exceed the
+        60s default, especially against a slower/emulated GROBID; raise it then.
 
     Returns
     -------
@@ -46,7 +50,7 @@ def extract_references(
     if grobid_url is None:
         grobid_url = Settings().grobid_url
 
-    with open(pdf_path, "rb") as fh, httpx.Client(timeout=60.0) as client:
+    with open(pdf_path, "rb") as fh, httpx.Client(timeout=timeout) as client:
         response = client.post(
             f"{grobid_url}/api/processReferences",
             files={"input": (pdf_path, fh, "application/pdf")},

codex/parsing/tex.py

@@ -17,6 +17,10 @@ _SECTION_RE = re.compile(
     re.DOTALL,
 )
 
+# \input{file} / \include{file} — arXiv papers routinely split the body across
+# files, so these must be inlined before parsing (R-C multi-file flattening).
+_INPUT_RE = re.compile(r"\\(?:input|include)\s*\{([^}]+)\}")
+
 # Patterns for LaTeX noise removal (applied in order).
 _COMMENT_RE = re.compile(r"%[^\n]*")
 _CITE_RE = re.compile(r"\\cite\*?\{[^}]*\}")
@@ -157,3 +161,63 @@ def latex_to_text(latex: str) -> str:
         return "\n\n".join(body for _, body in sections)
     # Fallback: no section structure — clean the whole string.
     return _clean_latex(latex)
+
+
+def _norm_texkey(name: str) -> str:
+    """Normalize a tex file name / ``\\input`` argument to a comparable key.
+
+    Strips a leading ``./``, any directory-irrelevant whitespace, and a trailing
+    ``.tex`` so ``\\input{sections/intro}`` matches the archive member
+    ``sections/intro.tex``.
+    """
+    n = name.strip()
+    if n.startswith("./"):  # a single leading "./" only — don't eat "../" or ".hidden"
+        n = n[2:]
+    return n[:-4] if n.endswith(".tex") else n
+
+
+def flatten_inputs(primary: str, files: dict[str, str]) -> str:
+    """Recursively inline ``\\input``/``\\include`` directives (R-C).
+
+    *files* maps each source file's archive name to its contents (keys may carry
+    a ``.tex`` suffix or a ``./`` prefix — they are normalized internally). arXiv
+    multi-file projects leave the ``\\documentclass`` file as little more than a
+    skeleton of ``\\input`` lines, so the body must be assembled before parsing.
+    Unresolved references are dropped; recursion is capped at depth 10 to guard
+    against include cycles.
+    """
+    norm = {_norm_texkey(k): v for k, v in files.items()}
+
+    def _expand(text: str, depth: int) -> str:
+        if depth > 10:
+            # Cap reached (likely an \input cycle): strip any still-unresolved
+            # directives rather than leak a literal "\input{…}" into the parsed text.
+            return _INPUT_RE.sub("", text)
+
+        def _repl(match: re.Match[str]) -> str:
+            content = norm.get(_norm_texkey(match.group(1)))
+            return _expand(content, depth + 1) if content is not None else ""
+
+        return _INPUT_RE.sub(_repl, text)
+
+    return _expand(primary, 0)
+
+
+def chunk_sections(latex: str, size: int = 512, overlap: int = 64) -> list[tuple[str | None, str]]:
+    """Chunk LaTeX *within* each section, pairing every chunk with its title.
+
+    Unlike :func:`latex_to_text` (which discards titles and flattens the whole
+    document into one block before word-window chunking), this keeps chunks from
+    spanning section boundaries and remembers which ``\\section`` each came from.
+    The caller can then label the stored ``section`` column from the real heading
+    instead of mostly ``body`` (R-C / audit R-12). Falls back to title-less
+    chunks of the whole cleaned document when there are no section commands.
+    """
+    sections = extract_sections(latex)
+    if not sections:
+        return [(None, chunk) for chunk in chunk_text(_clean_latex(latex), size, overlap)]
+    pairs: list[tuple[str | None, str]] = []
+    for title, body in sections:
+        for chunk in chunk_text(body, size, overlap):
+            pairs.append((title or None, chunk))
+    return pairs

codex/quality.py

@@ -110,6 +110,65 @@ def classify_section(text: str) -> str:
     return "body"
 
 
+def _clean_title(title: str) -> str:
+    """Normalize a LaTeX ``\\section`` title for use as a section label.
+
+    Strips LaTeX word-commands (``\\emph`` …), accent/escape macros (``\\"o`` →
+    ``o``, ``\\&``), ``~`` ties and ``{}$``, drops leading section numbering
+    (``3.2 ``), collapses whitespace, lower-cases, and truncates to 60 chars at a
+    word boundary so the stored ``section`` value is a clean, comparable string.
+    """
+    t = title.replace("~", " ")  # LaTeX non-breaking tie → space
+    t = re.sub(r"\\[a-zA-Z]+\*?", " ", t)  # word-commands: \emph, \mathcal …
+    t = re.sub(r"\\[^a-zA-Z]", "", t)  # accent/escape macros: \"o → o, \', \`, \&
+    t = re.sub(r"[{}$]", "", t)  # braces / math delimiters
+    t = re.sub(r"^\s*\d+(?:\.\d+)*\.?\s*", "", t)  # leading numbering "3.2 "
+    t = " ".join(t.split()).strip().lower()
+    return t[:60].rsplit(" ", 1)[0] if len(t) > 60 else t
+
+
+# A heading collapses to a controlled bucket only when it IS one of these canonical
+# section words — NOT when it merely starts with one. Prefix-matching via
+# classify_section mislabels real sections ("Abstract Nonsense and Categories" →
+# abstract, "References Architecture" → bibliography); an exact map avoids that while
+# keeping cross-source consistency for the bare headings.
+_SECTION_TITLE_BUCKETS = {
+    "abstract": "abstract",
+    "zusammenfassung": "abstract",
+    "introduction": "intro",
+    "einleitung": "intro",
+    "proof": "proof",
+    "beweis": "proof",
+    "references": "bibliography",
+    "bibliography": "bibliography",
+    "bibliographie": "bibliography",
+    "literatur": "bibliography",
+}
+
+
+def section_label(title: str | None, content: str) -> str:
+    """Label a chunk's section, preferring the real ``\\section`` heading (R-F).
+
+    For section-aware ``.tex`` ingest *title* is the real heading: a bare canonical
+    heading ("Introduction", "References", "Proof") maps to its controlled bucket
+    (cross-source consistency); any other heading is stored as its cleaned real
+    title (e.g. ``"preliminaries"``, ``"introduction to operator algebras"``) — far
+    more signal than collapsing to ``body`` AND without the prefix-match mislabels
+    that ``classify_section`` would produce on descriptive titles.
+
+    When *title* is None / blank (the ``.pdf`` / ``.txt`` / ``run_quality_pass``
+    paths) this falls back to content-based :func:`classify_section` — unchanged
+    behaviour. Safe to store free-text titles because the ``section`` column is
+    write-only (no consumer filters on the controlled vocabulary).
+    """
+    if not title or not title.strip():
+        return classify_section(content)
+    cleaned = _clean_title(title)
+    if not cleaned:
+        return classify_section(content)
+    return _SECTION_TITLE_BUCKETS.get(cleaned, cleaned)
+
+
 # ---------------------------------------------------------------------------
 # Batch filter
 # ---------------------------------------------------------------------------

codex/sources/arxiv.py

@@ -1,21 +1,110 @@
 """arXiv API client.
 
 Provides:
+- fetch_metadata: resolve an arXiv ID to a Paper via the Atom export API.
 - fetch_source: download the .tar.gz source of a paper and extract the primary .tex file.
 - fetch_pdf_url: return the canonical PDF URL for a given arXiv ID.
 """
 
 from __future__ import annotations
 
+import gzip
 import io
 import logging
 import tarfile
+import xml.etree.ElementTree as ET
 
 import httpx
+from tenacity import retry, retry_if_exception, stop_after_attempt, wait_exponential
+
+from codex.models import Paper
 
 logger = logging.getLogger(__name__)
 
 _BASE = "https://arxiv.org"
+_EXPORT = "https://export.arxiv.org"
+_ATOM = "{http://www.w3.org/2005/Atom}"
+
+
+def _is_retryable(exc: BaseException) -> bool:
+    if isinstance(exc, httpx.HTTPStatusError):
+        return exc.response.status_code == 429 or exc.response.status_code >= 500
+    return False
+
+
+@retry(
+    retry=retry_if_exception(_is_retryable),
+    stop=stop_after_attempt(4),
+    wait=wait_exponential(min=1, max=20),
+    before_sleep=lambda rs: logger.warning("arXiv retry %d", rs.attempt_number),
+)
+def _query(arxiv_id: str) -> httpx.Response:
+    response = httpx.get(
+        f"{_EXPORT}/api/query",
+        params={"id_list": arxiv_id},
+        timeout=30,
+        follow_redirects=True,
+    )
+    response.raise_for_status()
+    return response
+
+
+def fetch_metadata(arxiv_id: str) -> Paper | None:
+    """Resolve an arXiv ID to a Paper via the Atom export API.
+
+    Authoritative metadata source for arXiv preprints — used as an ingest
+    fallback when OpenAlex 404s on an arXiv id (DQ-2). The arXiv id (bare,
+    e.g. ``"1911.00966"`` or legacy ``"math/0603097"``) becomes ``Paper.id``;
+    ``openalex_id`` and ``bibkey`` are left for the caller to populate.
+
+    Returns
+    -------
+    Paper | None
+        Populated Paper (title, authors, year, abstract), or None if arXiv
+        has no entry for the id.
+    """
+    bare = arxiv_id[len("arxiv:") :] if arxiv_id.lower().startswith("arxiv:") else arxiv_id
+    try:
+        response = _query(bare)
+    except httpx.HTTPError:
+        logger.warning("arXiv metadata fetch failed for %s", bare, exc_info=True)
+        return None
+    try:
+        root = ET.fromstring(response.text)
+    except ET.ParseError:
+        return None
+    entry = root.find(f"{_ATOM}entry")
+    if entry is None:
+        return None
+    # An id-not-found query still returns a feed but with no <entry>.
+    title = (entry.findtext(f"{_ATOM}title") or "").strip()
+    if not title:
+        return None
+    summary = (entry.findtext(f"{_ATOM}summary") or "").strip()
+    published = entry.findtext(f"{_ATOM}published") or ""
+    year = int(published[:4]) if published[:4].isdigit() else None
+    authors = [
+        name.strip()
+        for a in entry.findall(f"{_ATOM}author")
+        if (name := a.findtext(f"{_ATOM}name")) and name.strip()
+    ]
+    return Paper(
+        id=bare,
+        title=" ".join(title.split()),
+        authors=authors,
+        year=year,
+        abstract=" ".join(summary.split()) or None,
+    )
+
+
+def _has_documentclass(content: str) -> bool:
+    """True if *content* has an UN-commented ``\\documentclass`` line.
+
+    A plain ``"\\documentclass" in content`` substring test also matches a
+    commented-out ``%\\documentclass`` (common in arXiv preambles); requiring the
+    command to start its line avoids selecting the wrong primary file.
+    """
+    return any(line.lstrip().startswith("\\documentclass") for line in content.splitlines())
 
 
 def fetch_source(arxiv_id: str) -> str | None:
@@ -23,8 +112,9 @@ def fetch_source(arxiv_id: str) -> str | None:
 
     Downloads the .tar.gz source bundle from ``https://arxiv.org/src/{arxiv_id}``,
     locates the primary .tex file (preferring any file containing ``\\documentclass``,
-    falling back to the largest .tex by size), and returns its contents as a UTF-8
+    falling back to the largest .tex by size), and inlines its ``\\input``/
-    string.
+    ``\\include`` directives from the other archive members so multi-file projects
+    return the full document body, not just the primary file's include skeleton.
 
     Parameters
     ----------
@@ -45,39 +135,58 @@ def fetch_source(arxiv_id: str) -> str | None:
     if response.status_code != 200:
         response.raise_for_status()
 
+    from codex.parsing.tex import flatten_inputs
+
     raw = response.content
+    # Image/font/binary members are never \input'd as text; skip them so the source
+    # map stays text-only (decode-with-replace would otherwise store garbled bytes).
+    skip_ext = (".png", ".jpg", ".jpeg", ".gif", ".bmp", ".pdf", ".eps", ".ps", ".ttf", ".otf")
     try:
         with tarfile.open(fileobj=io.BytesIO(raw), mode="r:gz") as tf:
-            tex_members = [m for m in tf.getmembers() if m.name.endswith(".tex")]
+            files: dict[str, str] = {}
-            if not tex_members:
+            primary_name: str | None = None
-                logger.debug("No .tex files found in arXiv source for %s", arxiv_id)
+            for member in tf.getmembers():
-                return None
+                if not member.isfile() or member.name.lower().endswith(skip_ext):
-
+                    continue
-            # Prefer the file containing \documentclass (primary document)
-            primary: tarfile.TarInfo | None = None
-            for member in tex_members:
                 f = tf.extractfile(member)
                 if f is None:
                     continue
-                content_bytes = f.read()
+                # Keep ALL text members resolvable so \input of a non-.tex include
-                if b"\\documentclass" in content_bytes:
+                # (e.g. a .def or extension-less body file) is not silently dropped (R-C).
-                    primary = member
+                files[member.name] = f.read().decode("utf-8", errors="replace")
-                    # Decode and return immediately — first match wins
+                # Primary doc = a .tex with an UN-commented \documentclass.
-                    return content_bytes.decode("utf-8", errors="replace")
+                if (
+                    primary_name is None
+                    and member.name.endswith(".tex")
+                    and _has_documentclass(files[member.name])
+                ):
+                    primary_name = member.name
 
-            if primary is None:
+            tex_files = {k: v for k, v in files.items() if k.endswith(".tex")}
-                # Fallback: largest .tex by size
+            if not tex_files:
-                largest = max(tex_members, key=lambda m: m.size)
+                logger.debug("No .tex files found in arXiv source for %s", arxiv_id)
-                f = tf.extractfile(largest)
+                return None
-                if f is None:
+
-                    return None
+            # No \documentclass anywhere → fall back to the largest .tex.
-                return f.read().decode("utf-8", errors="replace")
+            if primary_name is None:
-    except tarfile.TarError as exc:
+                primary_name = max(tex_files, key=lambda k: len(tex_files[k]))
-        logger.warning("Failed to open tar archive for %s: %s", arxiv_id, exc)
+
+            # Inline \input/\include so multi-file projects yield the full body,
+            # not just the primary file's skeleton of include directives (R-C).
+            return flatten_inputs(files[primary_name], files)
+    except tarfile.TarError:
+        # Old arXiv submissions are served as a single bare gzipped .tex with no
+        # tar wrapper (e.g. legacy math/* papers) — gunzip the body directly.
+        try:
+            single = gzip.decompress(raw).decode("utf-8", errors="replace")
+        except (OSError, EOFError) as exc:
+            logger.warning("Failed to read arXiv source for %s: %s", arxiv_id, exc)
+            return None
+        if "\\" in single[:5000]:  # looks like LaTeX (has backslash commands)
+            return single
+        logger.debug("arXiv source for %s is not LaTeX", arxiv_id)
         return None
 
-    return None  # unreachable but satisfies type checker
-
 
 def fetch_pdf_url(arxiv_id: str) -> str:
     """Return the canonical PDF URL for an arXiv paper.

codex/sources/crossref.py

@@ -0,0 +1,126 @@
+"""Crossref API client.
+
+Provides:
+- fetch_abstract: retrieve a work's abstract (JATS-stripped) by DOI.
+- fetch_references: retrieve a work's reference list (DOI edges) by DOI.
+
+Crossref is a *third* metadata source after OpenAlex and Semantic Scholar
+(DQ-2 abstracts / roadmap R-B references). Requests use the Polite Pool (mailto
+query parameter) and are retried on 429/5xx with exponential back-off via tenacity.
+"""
+
+from __future__ import annotations
+
+import logging
+import re
+from typing import Any
+
+import httpx
+from tenacity import retry, retry_if_exception, stop_after_attempt, wait_exponential
+
+from codex.config import get_settings
+from codex.models import Citation
+
+logger = logging.getLogger(__name__)
+
+_BASE = "https://api.crossref.org"
+_TAG_RE = re.compile(r"<[^>]+>")
+
+
+def _is_retryable(exc: BaseException) -> bool:
+    if isinstance(exc, httpx.HTTPStatusError):
+        return exc.response.status_code == 429 or exc.response.status_code >= 500
+    return False
+
+
+def _polite_params() -> dict[str, str]:
+    # Reuse the OpenAlex mailto for Crossref's Polite Pool (same address).
+    mailto = get_settings().openalex_mailto
+    return {"mailto": mailto} if mailto else {}
+
+
+@retry(
+    retry=retry_if_exception(_is_retryable),
+    stop=stop_after_attempt(5),
+    wait=wait_exponential(min=1, max=30),
+    before_sleep=lambda rs: logger.warning(
+        "Crossref retry %d after %s",
+        rs.attempt_number,
+        rs.outcome.exception(),  # type: ignore[union-attr]
+    ),
+)
+def _get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
+    merged: dict[str, str] = {**_polite_params(), **(params or {})}
+    response = httpx.get(url, params=merged, timeout=30, follow_redirects=True)
+    response.raise_for_status()
+    return response
+
+
+def _strip_jats(abstract: str | None) -> str | None:
+    """Strip JATS/XML tags from a Crossref abstract and collapse whitespace."""
+    if not abstract:
+        return None
+    text = _TAG_RE.sub("", abstract)
+    text = " ".join(text.split()).strip()
+    return text or None
+
+
+def fetch_abstract(doi: str) -> str | None:
+    """Fetch a work's abstract from Crossref by DOI.
+
+    Crossref stores abstracts as JATS-tagged markup (``<jats:p>…</jats:p>``);
+    tags are stripped before returning. Many works (notably book chapters)
+    have no abstract deposited — returns None in that case and on 404.
+
+    Parameters
+    ----------
+    doi:
+        A bare DOI (``"10.1007/s00454-019-00132-8"``).
+
+    Returns
+    -------
+    str | None
+        The plain-text abstract, or None when absent.
+    """
+    url = f"{_BASE}/works/{doi}"
+    try:
+        response = _get(url)
+    except httpx.HTTPStatusError as exc:
+        if exc.response.status_code == 404:
+            return None
+        raise
+    message: dict[str, Any] = response.json().get("message", {})
+    return _strip_jats(message.get("abstract"))
+
+
+def fetch_references(doi: str) -> list[Citation]:
+    """Fetch a work's reference list from Crossref by DOI (roadmap R-B).
+
+    Crossref carries publisher-deposited reference lists in ``message.reference``.
+    Each entry that cites a DOI-registered work exposes a bare ``DOI`` field;
+    only those become citation-graph edges (book / older references carry just
+    ``unstructured`` text with no resolvable id and are skipped). ``citing_id``
+    is the queried *doi* — the caller rewrites it to the canonical ``papers.id``
+    and normalises the cited DOIs (mirrors the Semantic Scholar reference path).
+
+    Parameters
+    ----------
+    doi:
+        A bare DOI (``"10.1007/s00454-019-00132-8"``).
+
+    Returns
+    -------
+    list[Citation]
+        One Citation per reference that carries a DOI. Empty on 404 or when no
+        references are deposited for the work.
+    """
+    url = f"{_BASE}/works/{doi}"
+    try:
+        response = _get(url)
+    except httpx.HTTPStatusError as exc:
+        if exc.response.status_code == 404:
+            return []
+        raise
+    message: dict[str, Any] = response.json().get("message", {})
+    references: list[dict[str, Any]] = message.get("reference") or []
+    return [Citation(citing_id=doi, cited_id=ref["DOI"]) for ref in references if ref.get("DOI")]

codex/sources/openalex.py

@@ -85,13 +85,55 @@ def _reconstruct_abstract(inverted_index: dict[str, list[int]] | None) -> str |
     return " ".join(w for _, w in word_positions)
 
 
+def _normalize_doi(doi: str) -> str:
+    """Normalize an OpenAlex DOI to the canonical bare, lower-cased form.
+
+    OpenAlex returns the ``doi`` field as a full URL
+    (``https://doi.org/10.1007/s00454-019-00132-8``), but the canonical
+    ``papers.id`` produced by the M-1 migration is the BARE, lower-cased DOI
+    (``10.1007/s00454-019-00132-8``). Stripping the ``https://doi.org/`` /
+    ``doi:`` prefix and lower-casing (DOIs are case-insensitive by spec) makes a
+    re-ingested DOI paper match its stored row, so the ingest
+    ``INSERT … ON CONFLICT (id)`` updates in place instead of attempting a fresh
+    INSERT that trips the separate ``papers_openalex_id_key`` unique constraint
+    (DQ-5). Mirrors the cited-id convention in ``ingest._norm_cited_id``.
+    """
+    s = doi.strip().lower()
+    for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):
+        if s.startswith(prefix):
+            return s[len(prefix) :]
+    return s
+
+
+# arXiv works are registered under a DOI of the form 10.48550/arXiv.<id>.
+_ARXIV_DOI_PREFIX = "10.48550/arxiv."
+
+
+def _canonical_id(doi: str) -> str:
+    """Return the canonical ``papers.id`` for an OpenAlex ``doi`` value.
+
+    Builds on :func:`_normalize_doi` (bare, lower-cased DOI), then strips the
+    arXiv DOI prefix ``10.48550/arxiv.`` so an arXiv work's id is the BARE arXiv
+    id (``2305.10988`` / ``math/0603097``) — the form the corpus is keyed on —
+    not the arXiv DOI. Without this, re-ingesting an arXiv paper by its bare id
+    misses ``INSERT … ON CONFLICT (id)`` and trips ``papers_openalex_id_key``.
+    This is the arXiv half of DQ-5 (the DOI half was fixed there; this was
+    explicitly deferred and surfaced again driving the R-C .tex re-ingest).
+    """
+    normalized = _normalize_doi(doi)
+    if normalized.startswith(_ARXIV_DOI_PREFIX):
+        return normalized[len(_ARXIV_DOI_PREFIX) :]
+    return normalized
+
+
 def _map_paper(data: dict[str, Any]) -> Paper:
     authors: list[str] = [
         a.get("author", {}).get("display_name") or "" for a in data.get("authorships", [])
     ]
     abstract = _reconstruct_abstract(data.get("abstract_inverted_index"))
+    doi = data.get("doi")
     return Paper(
-        id=data.get("doi") or data.get("id") or "",
+        id=_canonical_id(doi) if doi else (data.get("id") or ""),
         title=data.get("title") or "",
         openalex_id=data.get("id"),
         authors=authors,

codex/sources/semanticscholar.py

@@ -90,7 +90,11 @@ def fetch_references(paper_id: str) -> list[Citation]:
         raise
 
     data = response.json()
-    raw_refs: list[dict[str, Any]] = data.get("data", [])
+    # S2 returns HTTP 200 with ``{"data": null}`` for a known paper that has no
+    # parsed reference list (e.g. some theses). ``.get("data", [])`` would yield
+    # the explicit ``None`` (the default only applies when the key is absent),
+    # so iterate over a guaranteed list instead.
+    raw_refs: list[dict[str, Any]] = data.get("data") or []
     citations: list[Citation] = []
     for entry in raw_refs:
         cited_paper: dict[str, Any] = entry.get("citedPaper", {})
@@ -106,6 +110,24 @@ def fetch_references(paper_id: str) -> list[Citation]:
     return citations
 
 
+def fetch_abstract(paper_id: str) -> str | None:
+    """Fetch just the abstract for a paper from Semantic Scholar.
+
+    Used as an ingest abstract supplement (DQ-2) when OpenAlex has the paper
+    but no abstract. ``paper_id`` should be namespaced (``arXiv:…`` / ``DOI:…``).
+    Returns None on 404 or when S2 has no abstract.
+    """
+    url = f"{_BASE_GRAPH}/paper/{paper_id}"
+    try:
+        response = _get(url, params={"fields": "abstract"})
+    except httpx.HTTPStatusError as exc:
+        if exc.response.status_code == 404:
+            return None
+        raise
+    abstract = response.json().get("abstract")
+    return abstract or None
+
+
 def fetch_recommendations(paper_id: str, limit: int = 20) -> list[str]:
     """Fetch recommended paper IDs from Semantic Scholar.
 

docs/SESSION-2026-06-17-open-items.md

@@ -0,0 +1,59 @@
+# Open items — session 2026-06-17 (handoff notice)
+
+Everything still open after this session. Done items are in
+`docs/audit/DATA-QUALITY-2026-06-15.md` (DQ-1..DQ-5 + roadmap R-A,R-B,R-C,R-D,R-F all
+DONE; R-E deferred). This file is only the **loose ends**.
+
+## 1. ✅ RESOLVED — Jetson is online (the tunnel had dropped, not the host)
+- What looked like the Jetson going offline was the **SSH tunnel** breaking, not the
+  host. The Jetson (`192.168.178.103`) is online. Re-open the tunnel with keepalive:
+  `ssh -o ServerAliveInterval=15 -f -N -L 5433:localhost:5432 alfred@192.168.178.103`.
+  Better still: run long ops in tmux-on-Jetson (item #4) to avoid the tunnel entirely.
+
+## 2. ✅ DONE — R-F accent re-clean
+- R-F is functionally DONE (section signal 34/329 → **314/329 = 95 %**). The remaining
+  cosmetic accent/tie artifacts in live `chunks.section` labels were re-cleaned in place
+  once the tunnel was back: applied `codex.quality._clean_title` to every label
+  containing `\` or `~` — **8 labels fixed**, no re-embed. Verified **0 artifacts**
+  remain. R-F fully complete.
+
+## 3. ✅ READY TO MERGE — all branches integrated + validated
+All five feature branches are merged (**zero conflicts**) into **`integration/roadmap`**
+(off `audit/loop-1`) and validated green: **391 tests pass, ruff + ruff-format + mypy
+clean, tree clean**. This is the single merge candidate for `main`.
+
+Contents (DQ-1..DQ-5 + R-A..R-F + infra docs):
+| Source branch | Contents |
+|---|---|
+| `audit/loop-1` (base) | DQ-1..DQ-5, **R-A** (GROBID backfill + native arm64 GROBID), this notice |
+| `feat/section-labels` (incl. `feat/tex-ingest`) | **R-C** (.tex ingest) + DQ-5 arXiv-id fix + gzip fallback + **R-F** (section labels) |
+| `feat/crossref-references` | **R-B** (Crossref refs) + GROBID-on-demand tweak |
+| `feat/graph-coverage-warning` | **R-D** (citing-coverage warning) |
+| `chore/infra-ssh-stability` | infra TODO (#4) |
+
+**To land on `main`** (user-triggered):
+```
+git checkout main && git merge --no-ff integration/roadmap
+```
+…or open a PR `integration/roadmap` → `main`. The individual feature branches are
+preserved unchanged for per-feature review if preferred.
+
+**Cleanup — branches prunable AFTER the merge lands** (not deleted here; destructive):
+- Already in `main`: `fix/cli-readme-drift`, `fix/d04-d05-ingest-fixes`.
+- Folded into `integration/roadmap`: the 5 feature branches + `audit/loop-1`.
+- Pre-session / stale (verify before pruning): `feat/F-15-literature-graph`,
+  `feat/F-16-chunk-quality`, `fix/audit-wave-1`/`-2`/`-3`, `scratch/spike-embed`.
+- Working tree is clean — only gitignored `.venv`/caches/`.env`; no stray tracked files.
+
+## 4. Infra TODO — tmux-on-Jetson for stable long ops (documented, not implemented)
+- `docs/infra/jetson-ssh-stability.md` (branch `chore/infra-ssh-stability`). The
+  Mac↔Jetson tunnel dropped repeatedly on multi-minute writes all session. Fix: run long
+  ops **on the Jetson in `tmux`** (DB is localhost there → no tunnel; survives SSH drops);
+  `autossh` for interactive tunnels. Open.
+
+## 5. Known limitations (documented, NOT action items)
+- `math/0306167` (old AMS-TeX, no `\section{}`) stays `section=body` — inherent.
+- The 2 edited-volume books yielded 0 GROBID-parsed DOI/arXiv refs in the R-A sweep —
+  inherent (per-chapter refs, no clean end-bibliography).
+- **DQ-6** (upstream PDF→`.txt` extraction fidelity, done outside codex-py) — flagged
+  earlier, largely **mooted** by R-A/R-C ingesting from PDF/`.tex` directly.

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

@@ -1,6 +1,15 @@
 # DATA-QUALITY AUDIT — codex knowledge base (handoff for a fresh session)
 
-**Status:** baseline scan done 2026-06-15; four investigation items open (DQ-1…DQ-4).
+**Status:** baseline scan done 2026-06-15. **DQ-1 RESOLVED 2026-06-16** (S2 supplement
+applied to live DB + wired into ingest). **DQ-4 MEASURED 2026-06-16** — retrieval is
+strong after fixing a P0 `codex search paper` crash. **DQ-2 RESOLVED 2026-06-16**
+(1911.00966 fully recovered from arXiv; s00454 abstract from S2; book chapter is a
+documented limit; recovery wired into ingest). **DQ-3 RESOLVED 2026-06-16**
+(content fidelity clean — full coverage, only OCR junk dropped). **All four
+assessment items (DQ-1..DQ-4) DONE. DQ-5 RESOLVED 2026-06-17** (DOI id normalized
+to bare canonical form in `openalex._map_paper`; live re-ingest of
+`10.1007/s00454-019-00132-8` confirmed idempotent → **unblocks R-A/R-C**).
+**Roadmap R-A..R-E** added 2026-06-16 (free-source acquisition levers — see Roadmap section).
 **Author:** Audit-Loop (Opus). **Intended reader:** a *cold* session with no memory
 of the audit conversation — everything needed to continue is in this file.
 
@@ -50,7 +59,35 @@ incomplete, or unrepresentative data. This document is that second axis — a
 
 ## Findings (open investigation items)
 
-### DQ-1 — Citation coverage: 12 / 29 papers (41 %) have ZERO citations · **HIGH**
+### DQ-1 — Citation coverage: 12 / 29 papers (41 %) had ZERO citations · **RESOLVED 2026-06-16**
+
+**Resolution (what was done):**
+- **Verified upstream, not a bug.** Queried the OpenAlex API directly for all 11
+  zero-citation papers that have an `openalex_id`: every one returns
+  `referenced_works_count = 0` server-side, W-ids all match what we stored. They
+  are `type: preprint` (arXiv) / `article` / `dissertation` — works OpenAlex
+  indexes without a parsed bibliography. Confirmed source-coverage limit.
+- **Semantic Scholar supplement applied to the live DB** (idempotent backfill,
+  `ON CONFLICT (citing_id,cited_id) DO NOTHING`): **+330 citations (590 → 920)**.
+  Zero-out-edge papers **12 → 2**; in-corpus citing coverage **17/29 → 27/29**;
+  graph 489→704 nodes, 590→920 edges; discovery-lead targets 472→677. 9 of the
+  new edges are in-corpus (e.g. `2305.10988 → 10.1007/s00454-019-00132-8`).
+- **Wired into ingest** so future re-ingests self-heal: when OpenAlex returns an
+  empty `referenced_works`, `ingest.py` now falls back to
+  `_s2_reference_supplement()` (citing_id rewritten to canonical `papers.id`,
+  DOI cited-ids lowercased). Same helper drove the one-off backfill.
+- **Bug fixed (would have crashed the batch):** `semanticscholar.fetch_references`
+  used `data.get("data", [])`, but S2 returns HTTP 200 `{"data": null}` for a
+  known paper with no parsed refs (e.g. `depositonce-5415`) → `TypeError`.
+  Changed to `data.get("data") or []`. Removed a now-redundant discarded S2 probe
+  in the OpenAlex-404 arXiv branch. New regression test added.
+- **Irreducible remainder (documented limit):** the **2 `depositonce` theses**
+  (`10.14279/depositonce-20357`, `-5415`) stay at zero — neither OpenAlex nor S2
+  indexes references for TU-Berlin institutional DOIs. Accept as inherent.
+- **Files touched (uncommitted in working tree):** `codex/sources/semanticscholar.py`,
+  `codex/ingest.py`, `tests/ingest/test_ingest.py`. Full suite: 331 passed.
+
+**Original finding (for context):**
 - **Measured:** 12 papers contribute **no** out-edges; the 590-edge citation graph
   comes from only ~17 papers. The whole F-15 layer (PageRank / coupling /
   co-citation / discovery leads) therefore runs on ~59 % of the corpus.
@@ -79,7 +116,32 @@ incomplete, or unrepresentative data. This document is that second axis — a
   supplement, or (b) documented as an inherent OpenAlex-coverage limit with the
   graph caveated accordingly.
 
-### DQ-2 — Metadata gaps: 3 no-abstract, 1 fully metadata-less · **MED**
+### DQ-2 — Metadata gaps: 3 no-abstract, 1 fully metadata-less · **RESOLVED 2026-06-16**
+
+**Resolution (what was done):**
+- **`1911.00966` fully recovered** from the arXiv Atom API (OpenAlex 404'd on it):
+  title "A discrete version of Liouville's theorem on conformal maps",
+  Pinkall & Springborn, 2019, 384-char abstract → bibkey `PinkallSpringborn2019`
+  auto-generated, abstract embedded (non-zero). It was the worst node in the
+  corpus — now `@cite`-able, in wiki grounding, and its **10 chunks are visible
+  to chunk search** (previously filtered out by `bibkey IS NOT NULL`). Citations
+  were already added in DQ-1 (27 S2 refs).
+- **`10.1007/s00454-019-00132-8` abstract recovered from S2** (1186 chars) and
+  re-embedded (targeted `UPDATE`, not full re-ingest — see DQ-5).
+- **`10.1007/978-3-642-17413-1_7` (book chapter): documented inherent limit.**
+  No abstract in OpenAlex, S2, **or Crossref** (verified). Left as the single
+  remaining zero-vector paper; user may add an abstract by hand.
+- **Corpus now: 1 paper without abstract** (the book chapter), down from 3+1.
+  Zero-vector search pollution (DQ-4 secondary finding) reduced from 2 tail
+  fillers to 1.
+- **Wired into ingest** so this self-heals: OpenAlex-404 on an arXiv id now
+  recovers metadata via `arxiv.fetch_metadata` (new); an empty abstract is
+  supplemented via `_recover_abstract` → S2 then Crossref (new
+  `codex/sources/crossref.py`). New `semanticscholar.fetch_abstract`.
+- **Files touched:** `codex/sources/arxiv.py`, `codex/sources/crossref.py` (new),
+  `codex/sources/semanticscholar.py`, `codex/ingest.py`, + tests. Full suite: 342.
+
+**Original finding (for context):**
 - **Measured:**
   - **No abstract (3):** `10.1007/978-3-642-17413-1_7`,
     `10.1007/s00454-019-00132-8`, `1911.00966`. These get a **zero-vector**
@@ -98,7 +160,55 @@ incomplete, or unrepresentative data. This document is that second axis — a
 - **Acceptance:** every paper has at least a bibkey + non-zero abstract embedding,
   or the exceptions are documented with rationale.
 
-### DQ-3 — Content fidelity (chunks vs source `.txt`): NOT YET VERIFIED · **MED**
+### DQ-3 — Content fidelity (chunks vs source `.txt`): VERIFIED CLEAN · **RESOLVED 2026-06-16**
+
+**Resolution (read-only; re-ran `chunk_text` + `is_quality_chunk` on all 29
+source files and compared to stored chunks):**
+- **No paper is silently gutted.** Coverage (stored chunk chars / source chars)
+  is **109–114% for every paper** — the >100% is exactly the 64/512-word overlap
+  inflation, i.e. full retention. `stored == kept` for all 29, so the live DB
+  matches what the current pipeline produces.
+- **Only 18 chunks dropped corpus-wide, all `low_alpha`** (0 short, 0 bib),
+  concentrated in `10.1007/0-387-29555-0_13` (6) and `depositonce-5415` (10).
+  Inspected: they are **garbled OCR tables** from scanned-book sources (alpha
+  0.30–0.36, e.g. `"(u: 1) 7 < u D:= ud3424 — else H®: out.v. Family 1…"`) —
+  exactly the artefacts the alpha-ratio gate targets. **No real math content lost**
+  (the handoff's feared failure mode did not occur; math prose stays > 0.40 alpha).
+- **Head/tail alignment exact** on sampled papers: chunk 0 begins at the source
+  head (title/authors/abstract captured), last chunk ends at the source tail → no
+  front/back truncation.
+- **Note:** 0 bibliography drops across the corpus → the upstream `.txt` extraction
+  had already stripped reference lists, which is why DQ-1's citation graph relies
+  on the API/GROBID sources rather than text-mined refs.
+- **Acceptance met** for all 29 papers (not just a sample). No action needed.
+- **⚠ SCOPE LIMIT — DQ-3 covers `.txt → chunks` ONLY.** It treats each source
+  `.txt` as ground truth and verifies the *ingest pipeline* preserves it. It does
+  **not** measure the layer above — **PDF/source → `.txt`** — which was done by an
+  upstream tool in `ConformalLabpp` (outside codex-py) and is unexamined. There is
+  already evidence that layer is lossy: the 18 dropped chunks were garbled OCR
+  tables *already present in the `.txt`* (i.e. the PDF→txt step garbled the
+  table/formula regions), and the bibliographies were stripped upstream. So
+  "VERIFIED CLEAN" means **the loader faithfully preserves whatever the `.txt`
+  contains, not that no information was lost from the source paper.** See DQ-6.
+
+### DQ-6 — PDF/source → `.txt` extraction fidelity: NOT MEASURED · **MED, open**
+- **Open question:** how much did the upstream PDF→`.txt` extraction (done in
+  `ConformalLabpp`, outside codex-py) drop or garble vs the original papers?
+  Math/equations, tables, multi-column layouts, and figure captions are the usual
+  casualties of PDF text extraction — and we have direct evidence of garble
+  (DQ-3's low_alpha drops were already-garbled tables in the `.txt`).
+- **Checkable:** the 36 original PDFs are present in `…/ConformalLabpp/papers/`
+  (map each paper's `source_path` `.txt` to its sibling `.pdf` by filename stem).
+- **To investigate:** for a sample (incl. the known-bad scanned book
+  `0-387-29555-0_13` and a born-digital arXiv PDF), extract PDF text independently
+  and compare length / page-coverage to the `.txt`; spot-check whether specific
+  theorem statements & equations survive. Flag papers where the `.txt` is missing
+  large spans.
+- **Acceptance:** a per-sample source→txt coverage estimate, or a list of papers
+  whose `.txt` is materially degraded (candidates for re-extraction — note roadmap
+  **R-A/R-C** would re-ingest from PDF/`.tex` directly and largely sidestep this).
+
+**Original open question (for context):**
 - **Open question:** does the stored chunk set faithfully reconstruct each source
   file, or did the chunker / `filter_chunks` silently drop material (e.g. an
   abstract, a section, math-heavy passages)? The whole corpus was ingested from
@@ -111,7 +221,40 @@ incomplete, or unrepresentative data. This document is that second axis — a
 - **Acceptance:** sampled papers retain ≳ the expected fraction of source text;
   no paper is silently gutted by the quality gate.
 
-### DQ-4 — Retrieval quality: NOT YET MEASURED · **MED**
+### DQ-4 — Retrieval quality · **MEASURED 2026-06-16 — good, after fixing a P0 crash**
+
+**P0 bug found + fixed: `codex search paper` was crash-broken on the live DB.**
+The CLI passed the query embedding uncast, so pgvector raised
+`operator does not exist: vector <-> double precision[]` on every paper search.
+The working call sites (`mcp_server.py`, `wiki.py`) cast `%(emb)s::vector`; the
+CLI did not. Fixed both `<->` occurrences in `codex/cli.py search_paper`; added a
+regression guard in `tests/cli/test_cli.py` asserting the cast (mocked-DB unit
+tests can't catch the type error — this is why it survived the code audit).
+
+**Relevance verdict (post-fix): strong.** Six domain queries, both surfaces
+(paper-level abstract search + chunk-level). **rank-1 was the exactly-correct
+paper in 6/6 queries** for chunk search and 5/6 for paper-level (Laplace–Beltrami
+put the exact paper at rank-2 behind the closely-related "Polygon Laplacian Made
+Simple" — acceptable). Examples: "combinatorial Yamabe flow" → `math/0306167`
+(exact, all 5 top chunks that paper); "variational principle for Delaunay
+triangulations" → `math/0603097` (exact); "circle packing rigidity" →
+`2601.22903` (exact). Three of the DQ-1-rescued papers (`2305.10988`,
+`1005.2698`, `depositonce-5415`) now surface as top hits. The KB is trustworthy
+for lookups.
+
+**Secondary finding → reinforces DQ-2: zero-vector abstract pollution.** Papers
+with no abstract get a zero `abstract_emb`, which sits at constant L2 distance
+≈1.000 from every query and appears as filler in the paper-level tail whenever
+< 5 strongly-relevant papers exist. `1911.00966` (fully degraded, DQ-2) showed up
+at distance 1.000 in 4/6 queries. Harmless at rank>1 with a visible 1.000 score,
+but noise — and a concrete reason to fix DQ-2. Chunk-level search is immune (it
+filters `bibkey IS NOT NULL`, and 1911.00966 has no bibkey/chunks).
+
+**Note:** the MCP `search` docstring claims "hybrid dense + FTS" but the SQL is
+dense-only; `score = 1.0 - dist` can go negative (bge-m3 L2 ranges 0–2). Ranking
+is fine (monotonic); only the absolute score label is misleading.
+
+**Original open question (for context):**
 - **Open question:** end-to-end, do real queries return *relevant* results? Clean
   chunks + a working index don't guarantee useful retrieval.
 - **To investigate next:** run a handful of domain queries through the actual
@@ -123,16 +266,288 @@ incomplete, or unrepresentative data. This document is that second axis — a
 - **Acceptance:** a short relevance table (query → top-5 → on/off-topic) good
   enough to trust the KB for lookups, or a list of failure modes to fix.
 
+### DQ-5 — `ingest_paper` is NOT idempotent for DOI papers · **RESOLVED 2026-06-17** (found 2026-06-16)
+
+**Resolution (what was done):**
+- **Root-cause fix, minimal + contained:** added `openalex._normalize_doi()` and
+  applied it in `_map_paper` so the DOI branch yields the canonical **bare,
+  lower-cased** form (strips `https://doi.org/` / `http://doi.org/` / `doi:`;
+  lower-cases — DOIs are case-insensitive, matching `ingest._norm_cited_id`). The
+  no-DOI fallback (OpenAlex W-id URL) is left untouched. `_map_paper`→`fetch_paper`
+  →`ingest_paper` is the only consumer chain, so blast radius is one function.
+- **Checked nothing depended on the URL form.** It was the opposite: the full-URL
+  id silently *defeated* `_s2_id_for(paper.id)` and `_recover_abstract`'s
+  `paper.id.startswith("10.")` (a `https://…` string is neither `10.`- nor
+  `doi:`-prefixed), so S2/Crossref recovery never fired for DOI papers. The fix
+  repairs those paths too.
+- **Tests (offline, mocked DB):** closed audit **T-3** — the OpenAlex fixture now
+  emits the real URL-form DOI and asserts `paper.id` is the bare form; added
+  `_normalize_doi` unit tests (https/http/`doi:`/upper-case/already-bare) and a
+  W-id-fallback test; added ingest regression `test_ingest_doi_paper_upserts_bare
+  _canonical_id` (runs the real `_map_paper` through ingest, asserts the papers
+  upsert carries the **bare** id into `%(id)s` and uses `ON CONFLICT (id)`).
+  Verified it has teeth (fails on the pre-fix code). Full suite **348 passed**;
+  ruff + mypy --strict clean.
+- **Live idempotency confirmed (tunnel up):** re-ingested
+  `10.1007/s00454-019-00132-8` against the Jetson DB → no `UniqueViolation`;
+  `IngestResult(paper_id='10.1007/s00454-019-00132-8', citations_upserted=45)`.
+  After-state: **UPDATE in place** — `id` and `openalex_id` unchanged, **`added_at`
+  unchanged** (proves no fresh INSERT), exactly **1** row for the DOI (no URL-form
+  duplicate), citations 45→45, total papers 29→29.
+- **Unblocks R-A (GROBID re-ingest) and R-C (.tex re-ingest)** — both re-ingest
+  existing papers. **Files touched:** `codex/sources/openalex.py`,
+  `tests/sources/test_openalex.py`, `tests/ingest/test_ingest.py`.
+- **Note (out of scope, pre-existing):** arXiv papers stored as bare ids
+  (`2305.10988`) are still not round-trip idempotent if OpenAlex returns an
+  arXiv-DOI/W-id instead of the bare arXiv id — a separate canonicalization
+  concern, not this UniqueViolation. The DOI path (this finding) is fixed.
+
+**Original finding (for context):**
+- **Symptom:** re-ingesting an existing DOI paper crashes with
+  `UniqueViolation: papers_openalex_id_key`. Surfaced trying to re-ingest
+  `10.1007/s00454-019-00132-8` during the DQ-2 backfill.
+- **Root cause:** `openalex._map_paper` sets `Paper.id = data["doi"]`, which is the
+  **full URL** `https://doi.org/10.1007/…`. The stored canonical id is the **bare**
+  `10.1007/…` (post the M-1 canonical-id migration). So `INSERT … ON CONFLICT (id)`
+  finds no id match, attempts a fresh INSERT, and trips the *separate* unique
+  constraint on `openalex_id` (already held by the canonical-id row).
+- **Confirmed:** `openalex.fetch_paper("10.1007/s00454-019-00132-8").id ==
+  "https://doi.org/10.1007/s00454-019-00132-8"` (≠ stored bare id).
+- **Impact:** any re-ingest of a DOI paper aborts. This **blocks roadmap R-A
+  (GROBID on PDFs) and R-C (.tex ingest)** — both re-ingest existing papers. Also
+  implies *new* DOI ingests store full-URL ids, inconsistent with the bare-id
+  corpus (latent split-identity risk).
+- **Proposed fix (handle with care — M-1 incident territory):** normalize the DOI
+  in `_map_paper` to the canonical bare, lower-cased form (strip
+  `https://doi.org/`), matching what the M-1 migration produced. Add a re-ingest
+  idempotency test over a DOI paper. Did **not** fix inline this session — the
+  canonical-id derivation is exactly where the M-1 migration incident occurred, so
+  it needs its own focused change + a live re-ingest check.
+- **Workaround used for DQ-2:** targeted `UPDATE … SET abstract, abstract_emb`
+  instead of full re-ingest.
+
+---
+
+## Roadmap — data-acquisition levers (post-audit, all free sources)
+
+These are *forward-looking acquisition improvements*, distinct from the DQ-1..DQ-4
+audit findings (which assessed existing data). They came out of a strategy
+discussion on 2026-06-16: for this Math/CS corpus the valuable data (references,
+abstracts, full text) is almost entirely **open** (arXiv, OpenAlex, Crossref, S2),
+so the quality lever is *combining more free sources*, not buying paywall access.
+Paywall/uni-login was explicitly considered and **deferred** (see R-E). Each item
+is self-contained so a cold session can pick it up.
+
+### R-A — Run GROBID reference extraction on PDFs · **CORE DONE 2026-06-17** (full sweep optional)
+
+**Resolution (what was done) — citing coverage 27/29 → 29/29 (100%); edges 920 → 1022:**
+- **References-only backfill, not full re-ingest.** Added
+  [scripts/ra_grobid_backfill.py](../../scripts/ra_grobid_backfill.py): per paper,
+  run `grobid.extract_references(pdf)`, normalize cited-ids to the canonical bare
+  form (DOIs de-URL'd + lower-cased; `arXiv:` stripped), INSERT into `citations`
+  (`ON CONFLICT DO NOTHING`). Deliberately avoids `ingest_paper(source_path=pdf)`,
+  whose PDF branch re-runs Nougat + `DELETE FROM chunks` and would overwrite the
+  DQ-3-verified-clean `.txt` chunks (and needs Nougat). Idempotent; dry-run by
+  default; 7 tests; ruff/mypy clean.
+- **GROBID provisioning:** the pinned `grobid/grobid:0.8.2` is amd64-only, but the
+  Jetson and the dev Mac are both arm64 (this is why GROBID never ran). Ran the
+  lighter CRF image (`grobid/grobid:0.8.2-crf`) on the Mac under Podman+Rosetta
+  (PDFs are local; citations written over the SSH DB tunnel). Made
+  `extract_references` timeout configurable (theses need >60s emulated). A separate
+  task is provisioning a native arm64 GROBID on the Jetson (`docs/infra/grobid-jetson.md`).
+- **Both `depositonce` theses closed:** `…depositonce-20357` (lutz-2024) **+96**
+  edges (5 in-corpus); `…depositonce-5415` (sechelmann-2016) **+6** edges — its
+  147 MB/173-page scan blew pdfalto's 120s limit, so the 9 bibliography pages were
+  extracted with PyMuPDF first (77 refs, only 6 with a DOI/arXiv). **No paper has
+  zero out-edges now.**
+- **Optional remaining (secondary acceptance):** sweep the other 27 already-covered
+  papers for *extra* GROBID refs via `python scripts/ra_grobid_backfill.py --write`
+  (the 2 book PDFs need the same bib-page extraction as sechelmann).
+
+**Original plan (for context):**
+- **✓ Unblocked (DQ-5 RESOLVED 2026-06-17):** DOI re-ingest is now idempotent, so
+  the GROBID re-ingest no longer aborts on `papers_openalex_id_key`.
+- **What:** the whole corpus was ingested from `.txt` (`PAPERS_DIR=…/papers/txt`),
+  so the GROBID PDF path never ran. Re-ingest with a PDF `source_path` per paper
+  so `codex.parsing.grobid.extract_references` parses each bibliography.
+- **Why:** extracts references the APIs lack — a *complement* to DQ-1's S2
+  supplement. Crucially, the **2 `depositonce` theses** that stayed at zero in
+  DQ-1 (no API references anywhere) almost certainly have a references section in
+  their open-access PDFs → GROBID could finally give them out-edges. Closes the
+  last 2/29.
+- **How:** no new code — ingest already merges + dedups `api_citations +
+  pdf_citations` ([codex/ingest.py:288](../../codex/ingest.py)). GROBID server is
+  already configured (`GROBID_URL=http://192.168.178.103:8070` in
+  `.env.jetson-ingest`). Download free arXiv PDFs, re-ingest with `source_path`.
+- **Acceptance:** the 2 theses gain references; published papers gain
+  GROBID-parsed refs beyond OpenAlex/S2 coverage; citing coverage 27/29 → 29/29.
+
+### R-B — Add Crossref as a third citation + abstract source · **DONE 2026-06-17**
+
+**Resolution (what was done):**
+- **`crossref.fetch_references(doi)`** added (mirrors `semanticscholar.fetch_references`):
+  GETs `/works/{doi}`, returns one `Citation` per `message.reference[]` entry that
+  carries a registered `DOI` (book/`unstructured`-only refs are skipped — they
+  can't join the graph). `citing_id` is the queried DOI; the ingest supplement
+  rewrites it to `paper.id`.
+- **Wired as the third leg of the citation fallback chain** in `ingest.py`:
+  OpenAlex-empty → S2 → **Crossref** (`_crossref_reference_supplement`, DOI papers
+  only — Crossref's works endpoint is DOI-keyed). cited DOIs pass through
+  `_norm_cited_id` (bare, lower-cased). Network/parse failures degrade to [].
+- **Tests:** `fetch_references` unit tests (DOI edges / `unstructured` skipped / no
+  `reference` key / 404) + ingest tests asserting the Crossref leg fires when
+  OpenAlex+S2 are empty (cited DOI normalised) **and** does *not* fire when OpenAlex
+  has citations. Suite **361 green**, ruff/mypy clean. The DQ-2 abstract half
+  (`fetch_abstract`) already shipped earlier.
+- **Live-validated:** `fetch_references` against the real API returned 33 / 40 / 24
+  DOI-bearing refs for `10.1007/s00454-019-00132-8` / `10.1145/3132705` /
+  `10.1111/cgf.13931` (Springer / ACM / Wiley).
+- **No live corpus change (by design):** as a *fallback*, Crossref fires only when
+  OpenAlex **and** S2 are both empty. Post-DQ-1/R-A the only such papers were the 2
+  `depositonce` theses, which Crossref doesn't index either — so R-B is a
+  forward-looking third leg for future DOI ingests, not a backfill. (Harvesting
+  Crossref's *unique* refs for already-covered papers would need an always-merged
+  supplement instead — a deliberate scope choice not taken, per the doc's "fallback
+  chain" spec.) **Files:** `codex/sources/crossref.py`, `codex/ingest.py`, + tests.
+
+**Original plan (for context):**
+- **What:** new `codex.sources.crossref` client hitting Crossref REST
+  `/works/{doi}` for the `reference` array and `abstract`.
+- **Why:** Crossref carries **publisher-deposited references** for many DOIs (free,
+  polite pool via `mailto`) — a third leg after OpenAlex/S2. It also recovers
+  abstracts OpenAlex is contractually barred from redistributing (likely the 2
+  Springer DOIs missing abstracts in DQ-2). cited_ids are DOIs → flow through the
+  existing graph resolver unchanged.
+- **How:** mirror `codex/sources/openalex.py` (tenacity retry, polite pool). Extend
+  the ingest fallback chain to OpenAlex-empty → S2 → Crossref (same
+  `_s2_reference_supplement` shape). Add unit tests with mocked HTTP.
+- **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 · **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
+  boundaries. Directly serves **DQ-3** (content fidelity) and audit **R-12** (the
+  `section` column is low-signal because word-window `.txt` chunks rarely start at
+  a real header; `.tex` headers fix this).
+- **How:** download free arXiv source tarballs, feed `.tex` to ingest with
+  `source_path`. Handle multi-file projects (main `.tex` + includes).
+- **Acceptance:** `section` column gains signal (fewer `body`-only); DQ-3 coverage
+  vs source improves; no regression in the F-16 quality gate.
+
+### R-D — F-15: warn on low *citing-paper* coverage, not just paper count · **DONE 2026-06-17**
+
+**Resolution (what was done):**
+- Added `graph.citing_coverage(graph, known_ids)` → `(papers_with_out_edges,
+  total)`, a `graph_min_citing_coverage` setting (default 0.8), and wired both into
+  `codex graph report`: it now prints `Citing coverage: N/M papers with out-edges
+  (P%)` (and in `--json`), and emits a `Warning` when the share is below the
+  threshold ("low citing coverage weakens PageRank/coupling"). Separate from the
+  existing `graph_min_corpus_size` (total-count) warning.
+- Tests: `citing_coverage` unit tests + CLI tests (line shown; warning fires at
+  low coverage; suppressed at 100%; JSON field). Full suite green; ruff/mypy clean.
+- **Live:** `codex graph report` on the corpus prints `Citing coverage: 29/29
+  papers with out-edges (100%)` with no warning (post-R-A). Branch
+  `feat/graph-coverage-warning`. Files: `codex/config.py`, `codex/graph.py`,
+  `codex/cli.py`, + tests.
+
+**Original plan (for context):**
+- **What:** the open DQ-1 sub-item: `graph_min_corpus_size` only flags total paper
+  count. Add a warning when the share of papers with ≥1 out-edge is low (e.g.
+  < 80%), since that is what actually starves PageRank/coupling.
+- **Why:** at 17/29 the graph silently ran on 59% of the corpus with no signal.
+  Post-DQ-1 it's 27/29 (93%) — but the guard should catch future regressions.
+- **Acceptance:** `codex graph report` surfaces citing-coverage % and warns below
+  threshold.
+
+### R-E — Paywall / institutional access · **DEFERRED — only for a paywall-only expansion**
+- **Decision (2026-06-16):** a uni login does **not** help the current corpus —
+  every DQ-1/DQ-2 gap is in openly-available works (arXiv preprints, OA theses),
+  and all metadata/citation sources are free APIs. Revisit *only* if the corpus
+  expands to papers that exist solely behind a paywall with no preprint; then
+  institutional access → full-text PDF → GROBID refs (R-A) + clean chunks (R-C).
+- **ToS caveat:** manual download of individual papers you have legitimate access
+  to is fine; **automated bulk download through a uni proxy (EZproxy/Shibboleth)
+  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.
+
 ---
 
 ## Priority for the next session
-1. **DQ-1** (biggest lever — 41 % of the corpus is invisible to the graph; the S2
+1. ~~**DQ-1**~~ — **DONE 2026-06-16** (live DB at 920 citations, 27/29 citing
-   supplement is concrete and reuses existing code).
+   coverage; remedy wired into ingest).
-2. **DQ-4** (cheap, high-information — tells you if the KB is actually usable).
+2. ~~**DQ-4**~~ — **DONE 2026-06-16** (P0 `search paper` crash fixed; relevance
-3. **DQ-2**, then **DQ-3**.
+   verified strong; surfaced the zero-vector pollution that motivates DQ-2).
+3. ~~**DQ-2**~~ — **DONE 2026-06-16** (1911.00966 fully recovered; s00454 abstract
+   from S2; book chapter documented; recovery wired into ingest).
+4. ~~**DQ-3**~~ — **DONE 2026-06-16** (content fidelity clean; full coverage, only
+   18 OCR-junk chunks dropped, no math lost). **Assessment axis DQ-1..DQ-4 complete.**
+5. ~~**DQ-5**~~ — **DONE 2026-06-17** (DOI id normalized to bare form in
+   `openalex._map_paper`; live re-ingest of `10.1007/s00454-019-00132-8` idempotent
+   — UPDATE in place, `added_at` unchanged; suite 348 green). **Unblocks R-A/R-C.**
+6. **Roadmap levers** (see section above — now all unblocked): **R-A** (GROBID on
+   arXiv PDFs — closes the last 2 zero-citation theses), **R-B** (Crossref refs —
+   abstract half already shipped in DQ-2), **R-C** (`.tex` ingest — serves DQ-3),
+   **R-D** (F-15 coverage warning, quick). **R-E** (paywall) deferred.
 
-All four are *data* work (queries + maybe a re-ingest/enrichment), not code-audit
+DQ-1..DQ-4 are *data*/assessment work; DQ-5 + roadmap R-A..R-D add **new code**
-work — the code is already remediated (see the AUDIT-* docs and PRs #12–#14).
+(canonical-id fix, re-ingest scripts, Crossref references, a `.tex` path, a graph
+warning) on top of the already-remediated pipeline (see the AUDIT-* docs and PRs
+#12–#14). The DQ-1/DQ-2 ingest wiring + Crossref/arXiv abstract recovery already
+landed this session.
 
 ---
 

docs/infra/grobid-jetson.md

@@ -0,0 +1,192 @@
+# GROBID on the Jetson (aarch64) — deploy runbook
+
+**Status:** ACTIVE
+**Host:** `alfred@192.168.178.103` — NVIDIA Jetson Orin Nano (aarch64, 8 GB RAM, 8 GB swap, 6 cores)
+**Service:** GROBID reference extraction for roadmap **R-A** (`scripts/ra_grobid_backfill.py`)
+**Last updated:** 2026-06-17
+**Verified:** 2026-06-17 — `grobid/grobid:0.9.0-crf` pulled as native `arm64`, `/api/isalive`→`true`,
+end-to-end `extract_references` on `lutz-2024-thesis.pdf` → 116 refs (101 with DOI/arXiv) in ~36s.
+
+---
+
+## Why this image (`grobid/grobid:0.9.0-crf`)
+
+GROBID had never come up on the Jetson because `infra/docker-compose.yml` pinned
+`grobid/grobid:0.8.2`, and **every `0.8.x` tag (and the full `0.9.0`) is published
+amd64-only**. A Docker tag resolves to a multi-arch *manifest list*; on aarch64
+the `0.8.2` list has no `linux/arm64` entry, so there is simply nothing to pull or
+run (hence `curl localhost:8070` → connection refused, nothing listening).
+
+The fix is to select a tag whose manifest list actually contains a `linux/arm64`
+build:
+
+| Candidate                     | arm64? | Size    | Notes                                  |
+|-------------------------------|:------:|--------:|----------------------------------------|
+| `grobid/grobid:0.8.2`         | ✗      | ~9.5 GB | full DL image, amd64-only (old pin)    |
+| `grobid/grobid:0.9.0` / `-full`| ✗     | ~10 GB  | full DL image, amd64-only              |
+| **`grobid/grobid:0.9.0-crf`** | **✓**  | ~500 MB | **CRF-only, official, multi-arch** ←   |
+| `lfoppiano/grobid:0.9.0-crf`  | ✓      | ~500 MB | same build, community namespace (alt.) |
+
+We use **`grobid/grobid:0.9.0-crf`**:
+
+- **CRF-only** is sufficient for reference extraction (`/api/processReferences`)
+  and is ~500 MB vs ~10 GB for the deep-learning image.
+- **Native arm64** — no qemu emulation (too slow / RAM-heavy on a Jetson).
+- **Official namespace**, **pinned version** (not `latest-crf`, which is a moving
+  target). arm64 builds only exist from `0.9.0-crf` onward — there is no arm64
+  `0.8.x`, so this is a forced (but compatible) bump from the old `0.8.2` pin. The
+  TEI that `codex/parsing/grobid.py` parses (`biblStruct`, `persName`,
+  `idno[@type='DOI']`, …) is unchanged across the bump.
+
+> Caveat from upstream: the arm64 image is documented as "tested only on macOS,
+> not linux/arm64". The container is the *same* `linux/arm64` ELF either way, so
+> bare-metal Jetson works; the end-to-end check below is what de-risks it.
+
+---
+
+## One-time prerequisites
+
+### 1. Docker permission for `alfred`
+
+The SSH user `alfred` is in the `sudo` group but **not** the `docker` group, so
+`docker …` fails with `permission denied … /var/run/docker.sock`. Grant access
+once (requires the sudo password):
+
+```bash
+ssh alfred@192.168.178.103
+sudo usermod -aG docker alfred      # add to docker group (persistent)
+```
+
+Then **start a fresh login** so the new group takes effect (group membership is
+only re-evaluated at login — an existing session/`ssh` won't see it; a *new*
+`ssh` connection will):
+
+```bash
+exit && ssh alfred@192.168.178.103
+docker ps                            # should now work without sudo
+```
+
+(Alternatively run all `docker` commands below under `sudo`, but group membership
+is cleaner and lets `ra_grobid_backfill.py` / curl checks be driven over plain SSH.)
+
+### 2. Docker Compose v2 plugin (arm64)
+
+This host has Docker Engine but **not** the Compose v2 CLI plugin (on Linux they
+are separate packages; only Docker Desktop bundles Compose). Without it
+`docker compose …` fails with `docker: unknown command: docker compose`. Install
+the arm64 plugin into the user-local plugin dir (no sudo needed):
+
+```bash
+mkdir -p ~/.docker/cli-plugins
+curl -sSL https://github.com/docker/compose/releases/latest/download/docker-compose-linux-aarch64 \
+  -o ~/.docker/cli-plugins/docker-compose
+chmod +x ~/.docker/cli-plugins/docker-compose
+docker compose version               # confirm it resolves
+```
+
+---
+
+## Deploy
+
+GROBID is **service-scoped** on purpose: Postgres (`papers-db`) is already running
+on this host, so we bring up only the `grobid` service and never `docker compose up`
+the whole stack (that would try to start a second `papers-db`).
+
+```bash
+# copy this repo's compose file to the Jetson (first time only)
+scp infra/docker-compose.yml infra/schema.sql alfred@192.168.178.103:~/codex-infra/
+
+ssh alfred@192.168.178.103
+cd ~/codex-infra
+docker compose up -d grobid          # pulls grobid/grobid:0.9.0-crf (arm64), starts papers-grobid
+docker compose logs -f grobid        # wait for "Started ... in N seconds" (model load ~20–40s)
+```
+
+The `deploy.resources.limits.memory: 4g` cap in the compose file is honored by
+Compose v2 here (no swarm needed). 3 GB suffices for references; 4 GB leaves
+headroom alongside Postgres. The `restart: "no"` policy means GROBID does **not**
+auto-start on boot — see "Run on-demand" below.
+
+---
+
+## Run on-demand (stop when idle)
+
+GROBID is only needed **during reference extraction** (`scripts/ra_grobid_backfill.py`);
+nothing else in the stack uses it. Idle it still holds ~3.5 GB, so on the 8 GB Jetson
+keep it stopped and start it only for an R-A run:
+
+```bash
+ssh alfred@192.168.178.103 'docker start papers-grobid'        # ~30s model load
+curl -s --retry 30 --retry-delay 2 --retry-connrefused \
+  http://192.168.178.103:8070/api/isalive                      # wait for: true
+
+# ... run R-A from the Mac ...
+PYTHONPATH=. python scripts/ra_grobid_backfill.py --write
+
+ssh alfred@192.168.178.103 'docker stop papers-grobid'         # reclaim ~3.5 GB
+```
+
+First-time deploy uses `docker compose up -d grobid` (above); afterwards the
+container persists, so `docker start/stop papers-grobid` is all you need.
+
+> Why on-demand rather than a lighter tool: refextract was evaluated head-to-head
+> on the Jetson and rejected — far worse DOI recall on this math corpus (lutz
+> thesis: GROBID **101** usable IDs vs refextract **2**), and it was *slower* per
+> PDF despite a smaller footprint. GROBID stays; running it on-demand removes its
+> only real downside (idle RAM).
+
+---
+
+## Verify `GET /api/isalive` → `true`
+
+```bash
+# on the Jetson
+curl -s http://localhost:8070/api/isalive          # => true
+
+# from the Mac (LAN) — same value the corpus' GROBID_URL points at
+curl -s http://192.168.178.103:8070/api/isalive     # => true
+```
+
+Anything other than `true` (timeout / connection refused / `false`) means the
+container isn't up — check `docker compose logs grobid` and that nothing else
+holds port 8070.
+
+---
+
+## End-to-end reference-extraction check + running R-A
+
+With `GROBID_URL=http://192.168.178.103:8070` (already set in `.env.jetson-ingest`):
+
+```bash
+# one PDF, references only — should print N>0 parsed references
+PYTHONPATH=. python - <<'PY'
+from codex.parsing.grobid import extract_references
+refs = extract_references("/Users/tarikmoussa/Desktop/ConformalLabpp/papers/lutz-2024-thesis.pdf",
+                          grobid_url="http://192.168.178.103:8070")
+print(f"{len(refs)} references; first DOI/arXiv:",
+      next(((r['doi'], r['arxiv_id']) for r in refs if r['doi'] or r['arxiv_id']), None))
+PY
+```
+
+Then run the references-only backfill (DB tunnel up — see
+`docs/audit/DATA-QUALITY-2026-06-15.md`):
+
+```bash
+ssh -N -L 5433:localhost:5432 alfred@192.168.178.103 &     # DB tunnel
+cp .env.jetson-ingest .env
+PYTHONPATH=. python scripts/ra_grobid_backfill.py --zero-edge-only   # dry-run first
+PYTHONPATH=. python scripts/ra_grobid_backfill.py --write            # apply
+```
+
+---
+
+## Troubleshooting
+
+- **Container killed mid-request / exit 137** — OOM. The CRF image needs ~3 GB for
+  references; raise the compose `memory` limit or check Postgres isn't starving the
+  box (`free -h`, `docker stats papers-grobid`).
+- **`isalive` true but `processReferences` 500s** — usually a `pdfalto` failure on a
+  malformed PDF; confirm with a clean PDF (`lutz-2024-thesis.pdf`) and check
+  `docker compose logs grobid`.
+- **`permission denied … docker.sock`** — the docker-group prerequisite above wasn't
+  applied, or the SSH session predates it (re-login).

docs/infra/jetson-ssh-stability.md

@@ -0,0 +1,66 @@
+# Infra TODO — stable long-running ops against the Jetson (tmux + autossh)
+
+**Status:** OPEN (infra). **Filed:** 2026-06-17. **Priority:** MED — it slows live ops
+but has a known workaround (short/idempotent ops).
+
+## Problem (observed)
+
+Live data ops run on the **Mac** and reach the Jetson Postgres through an SSH
+port-forward tunnel (`ssh -f -N -L 5433:localhost:5432 alfred@192.168.178.103`,
+`DATABASE_URL` → `localhost:5433`). During the R-A / R-C / R-F work this tunnel
+**dropped repeatedly mid-run**: any operation longer than a few minutes (corpus
+re-ingest, the bge-m3 embed loop, the GROBID sweep) had a high chance of failing
+partway when the tunnel died, leaving the work half-applied. At one point the Jetson
+went **fully offline** (ping 100 % loss, `ssh:22` timeout) mid-operation.
+
+`ingest_paper()` and the backfill scripts open one DB connection for the whole run, so
+a tunnel drop raises `OperationalError: connection refused` and aborts — partial state,
+manual retry. Adding `ServerAliveInterval` to the tunnel helped only marginally.
+
+## Recommended fix
+
+**1. Run long ops *on the Jetson* inside `tmux` (primary fix).**
+The Jetson is where Postgres (and GROBID) live, so running ingest there means the DB is
+`localhost` — **no tunnel at all** — and `tmux` keeps the process alive across SSH
+disconnects (detach / reattach to monitor). This removes the tunnel from the critical
+path for every long-running write.
+
+- [ ] Confirm the `codex` env is deployable on the Jetson (Python 3.12+, deps incl. the
+      bge-m3 embedder; the Orin Nano GPU should handle it — GROBID already runs there).
+      If not, stand up a venv / container for it.
+- [ ] Standard pattern: `ssh alfred@jetson`, then
+      `tmux new -s codex` → `set -a; source .env; set +a` →
+      `PYTHONPATH=. python scripts/<job>.py --write` → detach (`Ctrl-b d`).
+      Reattach later with `tmux attach -t codex`. The job survives the SSH drop.
+- [ ] Point the Jetson-side `DATABASE_URL` at `localhost:5432` directly (no `:5433`).
+- [ ] Document this as the default for any multi-minute write (re-ingest, sweeps,
+      embed loops) in `docs/audit/DATA-QUALITY-2026-06-15.md` "How to reach the data".
+
+**2. `autossh` for when a tunnel *is* needed (secondary).**
+For interactive/dev use from the Mac (psql, quick probes, read-only queries), replace
+the plain `ssh -f -N -L` with `autossh -M 0 -f -N -o ServerAliveInterval=15 -o
+ServerAliveCountMax=3 -L 5433:localhost:5432 alfred@jetson` so a dropped tunnel
+auto-reconnects. NB: autossh only restarts the *tunnel* — an in-flight transaction
+still fails, so this is for short/interactive use, not long writes (use tmux-on-Jetson
+for those).
+
+**3. (Optional, code) make backfill scripts resilient.**
+Lower-value once (1)/(2) are in place, but: open a fresh `get_conn()` per paper (not one
+for the whole run) and/or wrap the per-item write in a small retry, so a transient drop
+costs one item, not the whole batch. The R-A backfill already does per-paper connections;
+`rc_tex_reingest.py` opens a connection per paper too — but `ingest_paper` itself holds
+one connection for its whole body, which is the unit that fails.
+
+## Why this matters
+
+The chronic flakiness directly cost time this session and left one cosmetic task
+unfinished (the R-F accent re-clean — see DATA-QUALITY-2026-06-15.md R-F "Pending"). The
+**robust pattern that already works** is short, idempotent operations (per-paper, or a
+single quick `UPDATE`); tmux-on-Jetson makes even the long ops safe.
+
+## Acceptance
+
+- A documented, repeatable way to run a full corpus re-ingest that survives an SSH drop
+  (tmux-on-Jetson), verified by detaching/reattaching across a disconnect.
+- The DATA-QUALITY doc's "How to reach the data" section recommends tmux-on-Jetson for
+  long writes and `autossh` for interactive tunnels.

infra/docker-compose.yml

@@ -28,20 +28,34 @@ services:
     restart: unless-stopped
 
   grobid:
-    # CRF-only image is sufficient for reference extraction and is lighter than
+    # CRF-only image: sufficient for reference extraction (/api/processReferences)
-    # the full deeplearning variant. Check https://hub.docker.com/r/grobid/grobid
+    # and ~500MB vs ~10GB for the full deep-learning variant.
-    # for the latest 0.8.x tag before deploying.
+    #
-    image: grobid/grobid:0.8.2
+    # The `-crf` tag is also the ONLY GROBID variant published as a multi-arch
+    # manifest that includes linux/arm64 — the full image (grobid/grobid:0.9.0)
+    # and every 0.8.x tag are amd64-only. So this is what lets GROBID run
+    # *natively* on the aarch64 Jetson (no slow/RAM-heavy qemu emulation). arm64
+    # builds start at 0.9.0-crf; there is no arm64 0.8.x.
+    # Deploy + docker-permission fix: docs/infra/grobid-jetson.md
+    image: grobid/grobid:0.9.0-crf
     container_name: papers-grobid
     ports:
       - "8070:8070"
-    restart: unless-stopped
+    init: true            # reap zombie children (GROBID docs recommend --init)
-    # GROBID is RAM-hungry; uncomment to cap usage on constrained hardware
+    ulimits:
-    # (e.g. Nvidia Jetson):
+      core: 0             # disable core dumps (GROBID docs: --ulimit core=0)
-    # deploy:
+    # On-demand only: GROBID is needed solely during reference extraction
-    #   resources:
+    # (scripts/ra_grobid_backfill.py), not for normal corpus operations — start it
-    #     limits:
+    # for an R-A run, stop it after to reclaim ~3.5GB. "no" = no auto-start on boot.
-    #       memory: 4g
+    # See docs/infra/grobid-jetson.md ("Run on-demand").
+    restart: "no"
+    # GROBID is RAM-hungry; cap usage on the constrained Jetson (Orin Nano, 8GB
+    # RAM shared with Postgres). 3GB suffices for references; 4g leaves headroom.
+    # Honored by `docker compose up` under Compose v2 (no swarm needed).
+    deploy:
+      resources:
+        limits:
+          memory: 4g
 
 volumes:
   pgdata:

scripts/__init__.py

@@ -0,0 +1 @@
+"""Operational one-off scripts (importable for tests)."""

scripts/ra_grobid_backfill.py

@@ -0,0 +1,227 @@
+"""R-A — GROBID reference backfill (references-only, idempotent).
+
+Adds GROBID-parsed citations to the live corpus **without** re-chunking the body,
+so the DQ-3-verified-clean ``.txt`` chunks are preserved. Complements the DQ-1
+Semantic-Scholar supplement with references the APIs lack (notably the two
+TU-Berlin ``depositonce`` theses, which neither OpenAlex nor S2 indexes).
+
+Why references-only instead of ``ingest_paper(source_path=pdf)``
+----------------------------------------------------------------
+The PDF branch of :func:`codex.ingest.ingest_paper` runs Nougat OCR and then
+``DELETE FROM chunks`` + re-INSERT — it would replace the clean ``.txt`` chunks
+(DQ-3) with unmeasured PDF-OCR text and additionally requires the Nougat server.
+This backfill touches only the ``citations`` table (``ON CONFLICT DO NOTHING``),
+so it is safe, idempotent, and needs only a reachable GROBID server.
+
+Prerequisite
+------------
+A reachable GROBID server. The corpus' ``GROBID_URL`` points at the Jetson
+(``http://192.168.178.103:8070``). GROBID now runs natively on that aarch64 host
+via the multi-arch CRF-only image (``grobid/grobid:0.9.0-crf``) — see
+``docs/infra/grobid-jetson.md`` for the deploy + docker-permission fix and the
+``GET /api/isalive`` check. (The old ``grobid/grobid:0.8.2`` pin was amd64-only,
+which is why GROBID never came up; pass ``--grobid-url`` to override the default.)
+Use the SSH DB tunnel for ``DATABASE_URL`` as documented in
+``docs/audit/DATA-QUALITY-2026-06-15.md``.
+
+Usage
+-----
+    # dry run (no writes) over the two zero-edge theses
+    PYTHONPATH=. python scripts/ra_grobid_backfill.py --zero-edge-only
+
+    # write every paper's GROBID-parsed refs to the live DB
+    PYTHONPATH=. python scripts/ra_grobid_backfill.py --write
+
+Default is **dry-run**; pass ``--write`` to mutate the live DB.
+"""
+
+from __future__ import annotations
+
+import argparse
+import logging
+from pathlib import Path
+
+import psycopg
+import psycopg.rows
+
+from codex.config import get_settings
+from codex.db import get_conn
+from codex.models import Citation
+from codex.parsing.grobid import extract_references
+
+logger = logging.getLogger(__name__)
+
+DEFAULT_PDF_DIR = "/Users/tarikmoussa/Desktop/ConformalLabpp/papers"
+
+
+def _normalize_cited_id(doi: str = "", arxiv_id: str = "") -> str | None:
+    """Normalize a GROBID-extracted reference id to the corpus' canonical form.
+
+    DOIs → bare, lower-cased (strip ``https://doi.org/`` / ``http://`` / ``doi:``),
+    matching ``papers.id`` and ``codex.sources.openalex._normalize_doi`` (DQ-5).
+    arXiv ids → strip a leading ``arXiv:`` prefix, leaving the bare id
+    (``2305.10988``, ``math/0603097``). DOI takes precedence when both exist.
+    Kept self-contained rather than reusing ``ingest._norm_cited_id`` because it
+    additionally strips the ``arXiv:`` prefix (which GROBID can emit but that
+    helper leaves untouched), and to avoid importing a private cross-module name.
+    """
+    doi = (doi or "").strip()
+    if doi:
+        s = doi.lower()
+        for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):
+            if s.startswith(prefix):
+                return s[len(prefix) :]
+        return s
+    arx = (arxiv_id or "").strip()
+    if arx:
+        return arx[len("arxiv:") :].strip() if arx.lower().startswith("arxiv:") else arx
+    return None
+
+
+def build_grobid_citations(
+    paper_id: str,
+    pdf_path: str | Path,
+    grobid_url: str | None = None,
+    timeout: float = 60.0,
+) -> list[Citation]:
+    """Extract a paper's references via GROBID and return normalized Citations.
+
+    ``citing_id`` is the canonical ``paper_id``; ``cited_id`` is normalized.
+    Self-citations and within-paper duplicates are dropped. Refs with neither a
+    DOI nor an arXiv id are skipped (they cannot join the graph).
+    """
+    refs = extract_references(str(pdf_path), grobid_url=grobid_url, timeout=timeout)
+    seen: set[str] = set()
+    citations: list[Citation] = []
+    for ref in refs:
+        cited = _normalize_cited_id(ref.get("doi", ""), ref.get("arxiv_id", ""))
+        if not cited or cited == paper_id or cited in seen:
+            continue
+        seen.add(cited)
+        citations.append(Citation(citing_id=paper_id, cited_id=cited))
+    return citations
+
+
+def _coverage(conn: psycopg.Connection[psycopg.rows.DictRow]) -> tuple[int, int, int]:
+    """Return (n_papers, n_papers_with_out_edges, n_citations) from the live DB."""
+    row = conn.execute(
+        """
+        SELECT (SELECT count(*) FROM papers)                    AS papers,
+               (SELECT count(DISTINCT citing_id) FROM citations) AS citing,
+               (SELECT count(*) FROM citations)                  AS edges
+        """
+    ).fetchone()
+    assert row is not None
+    return int(row["papers"]), int(row["citing"]), int(row["edges"])
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--pdf-dir", default=DEFAULT_PDF_DIR, help="directory of source PDFs")
+    parser.add_argument("--grobid-url", default=None, help="override Settings().grobid_url")
+    parser.add_argument("--only", default=None, help="restrict to a single paper id")
+    parser.add_argument(
+        "--zero-edge-only",
+        action="store_true",
+        help="only papers with 0 out-edges (the R-A primary targets)",
+    )
+    parser.add_argument("--limit", type=int, default=None, help="cap number of papers")
+    parser.add_argument(
+        "--timeout",
+        type=float,
+        default=300.0,
+        help="GROBID HTTP timeout (s); theses can need >60s, esp. emulated",
+    )
+    parser.add_argument(
+        "--write", action="store_true", help="WRITE to the live DB (default: dry-run)"
+    )
+    args = parser.parse_args(argv)
+
+    logging.basicConfig(level=logging.INFO, format="%(levelname)s %(message)s")
+    grobid_url = args.grobid_url or get_settings().grobid_url
+    pdf_dir = Path(args.pdf_dir)
+    pdfs = {p.stem: p for p in pdf_dir.glob("*.pdf")}
+
+    # Read the target list in a short-lived connection, then release it: the GROBID
+    # extraction below is a slow per-paper network loop and must NOT hold an
+    # idle-in-transaction connection open across it (a mid-loop SSH-tunnel drop would
+    # otherwise abort the whole batch — see docs/infra/jetson-ssh-stability.md).
+    with get_conn() as conn:
+        rows = conn.execute(
+            """
+            SELECT p.id, p.source_path,
+                   (SELECT count(*) FROM citations ci WHERE ci.citing_id = p.id) AS out_edges
+            FROM papers p
+            ORDER BY out_edges, p.id
+            """
+        ).fetchall()
+
+    targets: list[tuple[str, Path]] = []
+    for r in rows:
+        if args.only and r["id"] != args.only:
+            continue
+        if args.zero_edge_only and r["out_edges"] != 0:
+            continue
+        stem = Path(r["source_path"]).stem if r["source_path"] else None
+        pdf = pdfs.get(stem) if stem else None
+        if pdf is None:
+            logger.warning("no PDF for %s (stem=%s) — skipping", r["id"], stem)
+            continue
+        targets.append((r["id"], pdf))
+    if args.limit is not None:
+        targets = targets[: args.limit]
+
+    logger.info(
+        "GROBID=%s | papers to process=%d | mode=%s",
+        grobid_url,
+        len(targets),
+        "WRITE" if args.write else "DRY-RUN",
+    )
+
+    # GROBID extraction — no DB connection held during this slow network loop.
+    all_citations: list[Citation] = []
+    for paper_id, pdf in targets:
+        try:
+            cits = build_grobid_citations(
+                paper_id, pdf, grobid_url=grobid_url, timeout=args.timeout
+            )
+        except Exception as exc:
+            logger.warning("GROBID extraction failed for %s (%s): %s", paper_id, pdf.name, exc)
+            continue
+        logger.info("%-38s %3d refs  (%s)", paper_id, len(cits), pdf.name)
+        all_citations.extend(cits)
+
+    logger.info("total candidate citations: %d", len(all_citations))
+
+    if not args.write:
+        logger.info("DRY-RUN — no rows written. Re-run with --write to apply.")
+        return 0
+
+    # Fresh connection for the write — the read connection was already released.
+    with get_conn() as conn:
+        before = _coverage(conn)
+        with conn.cursor() as cur:
+            cur.executemany(
+                """
+                INSERT INTO citations (citing_id, cited_id, context)
+                VALUES (%s, %s, %s)
+                ON CONFLICT (citing_id, cited_id) DO NOTHING
+                """,
+                [(c.citing_id, c.cited_id, c.context) for c in all_citations],
+            )
+        conn.commit()
+        after = _coverage(conn)
+    logger.info(
+        "coverage papers=%d  citing %d->%d  edges %d->%d (+%d)",
+        after[0],
+        before[1],
+        after[1],
+        before[2],
+        after[2],
+        after[2] - before[2],
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

scripts/rc_tex_reingest.py

@@ -0,0 +1,131 @@
+"""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()
+    # Exclude DOIs (incl. the arXiv DOI 10.48550/arXiv.*), OpenAlex W-ids, and any
+    # http(s) URL form; everything else is treated as a bare arXiv id.
+    return (
+        bool(p)
+        and not p.startswith(("10.", "W"))
+        and not p.lower().startswith(("http://", "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())

tests/cli/test_cli.py

@@ -106,6 +106,13 @@ class TestSearch:
             assert "Test Paper" in result.stdout
             assert "0.123" in result.stdout
 
+            # Regression guard (DQ-4): the pgvector `<->` operator requires the
+            # query embedding cast to ::vector. Without it, real Postgres raises
+            # "operator does not exist: vector <-> double precision[]". Mocked DBs
+            # don't catch the type error, so assert the cast is in the SQL.
+            executed_sql = mock_conn.execute.call_args_list[0][0][0]
+            assert "<->" in executed_sql and "::vector" in executed_sql
+
     def test_search_formula_command(self) -> None:
         """Test `search formula` command with mocked DB."""
         with patch("codex.db.get_conn") as mock_get_conn:

tests/graph/test_cli.py

@@ -119,6 +119,36 @@ class TestGraphReport:
         assert result.exit_code == 0
         assert "Warning" in result.output or "warning" in result.output
 
+    def test_shows_citing_coverage_line(self):
+        # _sample_graph: A, B, C all cite → 3/3 = 100%, so the line shows but no warning.
+        out = self._run(known_ids=("A", "B", "C")).output
+        assert "Citing coverage" in out
+        assert "weakens" not in out  # 100% coverage → no R-D warning
+
+    def test_low_citing_coverage_warning(self):
+        # Only A has an out-edge; B and C are ingested but cite nothing → 1/3 = 33%.
+        g = nx.DiGraph()
+        g.add_edge("A", "X")
+        g.add_nodes_from(["B", "C"])
+        result = self._run(graph=g, known_ids=("A", "B", "C"))
+        assert result.exit_code == 0
+        assert "weakens PageRank" in result.output  # the R-D coverage warning
+
+    def test_json_includes_citing_coverage(self):
+        import json
+
+        g = nx.DiGraph()
+        g.add_edge("A", "X")
+        g.add_nodes_from(["B", "C"])
+        conn = _make_conn_with_paper_ids("A", "B", "C")
+        with (
+            patch("codex.db.get_conn", side_effect=_make_conn_cm(conn)),
+            patch("codex.graph.build_citation_graph", return_value=g),
+        ):
+            result = runner.invoke(app, ["graph", "report", "--json"])
+        data = json.loads(result.output)
+        assert data["citing_coverage"] == {"citing": 1, "papers": 3, "fraction": 0.3333}
+
 
 # ---------------------------------------------------------------------------
 # codex graph related

tests/graph/test_graph.py

@@ -10,6 +10,7 @@ import pytest
 from codex.graph import (
     build_citation_graph,
     citation_pagerank,
+    citing_coverage,
     dangling_citations,
     find_co_cited,
     find_related,
@@ -287,3 +288,24 @@ class TestDanglingCitations:
         g = build_citation_graph(_make_conn(rows))
         dangling = dangling_citations(g, set())
         assert set(dangling) == {"A", "B"}
+
+
+# ---------------------------------------------------------------------------
+# citing_coverage (R-D)
+# ---------------------------------------------------------------------------
+
+
+class TestCitingCoverage:
+    def test_counts_papers_with_out_edges(self):
+        # _small_graph: A→.., B→.., C→D have out-edges; D, E have none.
+        g = _small_graph()
+        n_citing, n_papers = citing_coverage(g, {"A", "B", "C", "D", "E"})
+        assert (n_citing, n_papers) == (3, 5)
+
+    def test_paper_absent_from_graph_counts_as_no_out_edges(self):
+        # A cites; Z was ingested but has no chunks/edges, so it isn't a graph node.
+        g = _small_graph()
+        assert citing_coverage(g, {"A", "Z"}) == (1, 2)
+
+    def test_empty(self):
+        assert citing_coverage(nx.DiGraph(), set()) == (0, 0)

tests/ingest/test_ingest.py

@@ -10,6 +10,7 @@ from contextlib import contextmanager
 from typing import Any
 from unittest.mock import MagicMock, patch
 
+import httpx
 import numpy as np
 import psycopg
 import pytest
@@ -107,6 +108,60 @@ def test_ingest_paper_basic() -> None:
     )
 
 
+def test_ingest_citation_fallback_to_crossref() -> None:
+    """R-B: OpenAlex + S2 both empty → Crossref references supply the edges.
+
+    Crossref is the third leg of the fallback chain. Its cited DOIs are
+    case-normalised and citing_id is rewritten to the canonical paper.id.
+    """
+    paper = _make_paper(paper_id="10.1007/s00454-019-00132-8", openalex_id="W123")
+    mock_conn = MagicMock()
+    mock_conn.execute = MagicMock()
+    mock_conn.executemany = MagicMock()
+    mock_conn.commit = MagicMock()
+
+    # Upper-case suffix proves the cited DOI is normalised to bare lower-case.
+    crossref_refs = [Citation(citing_id=paper.id, cited_id="10.1090/S0002-9947-04-03545-7")]
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=paper),
+        patch("codex.ingest.openalex.fetch_citations", return_value=[]),  # OpenAlex empty
+        patch("codex.ingest.semanticscholar.fetch_references", return_value=[]),  # S2 empty
+        patch("codex.ingest.crossref.fetch_references", return_value=crossref_refs) as mock_cr,
+        patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        result = ingest_paper(paper.id)
+
+    # Crossref consulted with the bare DOI; one edge upserted.
+    mock_cr.assert_called_once_with(paper.id)
+    assert result.citations_upserted == 1
+    mock_cursor = mock_conn.cursor.return_value.__enter__.return_value
+    cit_rows = mock_cursor.executemany.call_args_list[0][0][1]
+    assert cit_rows[0][0] == paper.id
+    assert cit_rows[0][1] == "10.1090/s0002-9947-04-03545-7"
+
+
+def test_ingest_crossref_not_called_when_openalex_has_citations() -> None:
+    """R-B: the Crossref leg fires only when OpenAlex+S2 are empty (it's a fallback)."""
+    paper = _make_paper(paper_id="10.1007/s00454-019-00132-8", openalex_id="W123")
+    mock_conn = MagicMock()
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=paper),
+        patch(
+            "codex.ingest.openalex.fetch_citations",
+            return_value=[Citation(citing_id="W123", cited_id="https://openalex.org/W9")],
+        ),
+        patch("codex.ingest.crossref.fetch_references") as mock_cr,
+        patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        ingest_paper(paper.id)
+
+    mock_cr.assert_not_called()
+
+
 def test_ingest_canonicalises_paper_id_to_caller_arg() -> None:
     """papers.id is the caller-supplied id, not OpenAlex's URL-form id (audit C-7).
 
@@ -144,7 +199,8 @@ def test_ingest_canonicalises_paper_id_to_caller_arg() -> None:
 
 
 def test_ingest_paper_source_tex(tmp_path: Any) -> None:
-    """``.tex`` source → latex_to_text, chunk_text, embed, chunks inserted in DB."""
+    """``.tex`` source → section-aware chunking; the stored ``section`` column is
+    labelled from the real ``\\section`` heading, not the chunk body (R-C / R-12)."""
     tex_file = tmp_path / "paper.tex"
     tex_file.write_text(r"\section{Introduction} Hello world. This is a test paper.")
 
@@ -154,16 +210,20 @@ def test_ingest_paper_source_tex(tmp_path: Any) -> None:
     mock_conn.executemany = MagicMock()
     mock_conn.commit = MagicMock()
 
-    fake_chunks = ["chunk one text here.", "chunk two text here."]
+    # (section title, chunk content) pairs from the section-aware chunker.
+    section_pairs = [
+        ("Introduction", "Body of the introduction goes here."),
+        ("Proof of the Main Theorem", "Body of the proof goes here."),
+        ("3.2 Discrete Conformal Maps", "Body about discrete conformal maps."),
+    ]
 
     with (
         patch("codex.ingest.openalex.fetch_paper", return_value=paper),
         patch("codex.ingest.openalex.fetch_citations", return_value=[]),
         patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
         patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
-        patch("codex.parsing.tex.latex_to_text", return_value="Hello world. Intro text."),
+        patch("codex.parsing.tex.chunk_sections", return_value=section_pairs),
-        patch("codex.parsing.tex.chunk_text", return_value=fake_chunks),
+        patch("codex.ingest.is_quality_chunk", return_value=True),
-        patch("codex.ingest.filter_chunks", side_effect=lambda chunks, settings: chunks),
     ):
         result = ingest_paper(paper.id, source_path=str(tex_file))
 
@@ -178,7 +238,16 @@ def test_ingest_paper_source_tex(tmp_path: Any) -> None:
     chunk_sql: str = chunk_insert_call[0][0]
     assert "INSERT INTO chunks" in chunk_sql
 
-    assert result.chunks_upserted == len(fake_chunks)
+    # R-F: a bare canonical heading → bucket ("Introduction"→intro); any other
+    # heading is stored as its cleaned real title ("proof of the main theorem",
+    # "discrete conformal maps") instead of being collapsed/mislabelled.
+    chunk_rows = chunk_insert_call[0][1]
+    assert [row[4] for row in chunk_rows] == [
+        "intro",
+        "proof of the main theorem",
+        "discrete conformal maps",
+    ]
+    assert result.chunks_upserted == len(section_pairs)
 
 
 # ---------------------------------------------------------------------------
@@ -206,12 +275,15 @@ def test_ingest_paper_source_pdf(tmp_path: Any) -> None:
     with (
         patch("codex.ingest.openalex.fetch_paper", return_value=paper),
         patch("codex.ingest.openalex.fetch_citations", return_value=[]),
+        # OpenAlex empty → ingest now consults the S2 reference supplement (DQ-1);
+        # mock it empty so only the GROBID refs contribute to the count.
+        patch("codex.ingest.semanticscholar.fetch_references", return_value=[]),
         patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
         patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
         patch("codex.parsing.nougat.pdf_to_markdown", return_value="pdf markdown text."),
         patch("codex.parsing.tex.chunk_text", return_value=fake_chunks),
         patch("codex.parsing.grobid.extract_references", return_value=grobid_refs),
-        patch("codex.ingest.filter_chunks", side_effect=lambda chunks, settings: chunks),
+        patch("codex.ingest.is_quality_chunk", return_value=True),
     ):
         result = ingest_paper(paper.id, source_path=str(pdf_file))
 
@@ -227,6 +299,73 @@ def test_ingest_paper_source_pdf(tmp_path: Any) -> None:
     assert mock_cursor.executemany.call_count >= 2
 
 
+def test_ingest_pdf_grobid_citations_normalize_doi(tmp_path: Any) -> None:
+    """R-A guard: GROBID extracts the DOI verbatim from the PDF reference text, so
+    it may be mixed-case, a ``https://doi.org/…`` URL, or ``doi:``-prefixed. Each
+    must be normalized to the bare, lower-cased canonical form before the Citation
+    is built — otherwise the same reference splits into case-/URL-variant graph
+    nodes that never join the bare-lowercase ``papers.id``. arXiv-only refs (no
+    DOI) are left untouched. Mirrors the S2-supplement normalization (DQ-1)."""
+    pdf_file = tmp_path / "paper.pdf"
+    pdf_file.write_bytes(b"%PDF-1.4 fake content")
+
+    paper = _make_paper()
+    mock_conn = MagicMock()
+    mock_conn.execute = MagicMock()
+    mock_conn.executemany = MagicMock()
+    mock_conn.commit = MagicMock()
+
+    def _ref(doi: str = "", arxiv_id: str = "") -> dict[str, str]:
+        # Faithful to GROBID's output shape: all five keys always present.
+        return {"title": "", "authors": "", "year": "", "doi": doi, "arxiv_id": arxiv_id}
+
+    grobid_refs = [
+        _ref(doi="10.1007/S00454-019-00132-8"),  # mixed-case bare DOI
+        _ref(doi="https://doi.org/10.1145/AbC.123"),  # URL-form DOI
+        _ref(doi="doi:10.1/MixedCase"),  # doi:-prefixed DOI
+        _ref(arxiv_id="2101.00001"),  # arXiv-only ref → untouched
+    ]
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=paper),
+        patch("codex.ingest.openalex.fetch_citations", return_value=[]),
+        # OpenAlex empty → S2 supplement consulted (DQ-1); empty so only GROBID
+        # refs contribute to the citation rows under inspection.
+        patch("codex.ingest.semanticscholar.fetch_references", return_value=[]),
+        patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+        patch("codex.parsing.nougat.pdf_to_markdown", return_value="pdf markdown text."),
+        patch("codex.parsing.tex.chunk_text", return_value=["pdf chunk one."]),
+        patch("codex.parsing.grobid.extract_references", return_value=grobid_refs),
+        patch("codex.ingest.is_quality_chunk", return_value=True),
+    ):
+        result = ingest_paper(paper.id, source_path=str(pdf_file))
+
+    assert result.citations_upserted == 4
+
+    # Locate the citations INSERT among the cursor's executemany calls (chunks
+    # are also inserted via executemany, so filter by SQL rather than by index).
+    mock_cursor = mock_conn.cursor.return_value.__enter__.return_value
+    citation_calls = [
+        c for c in mock_cursor.executemany.call_args_list if "INSERT INTO citations" in c[0][0]
+    ]
+    assert len(citation_calls) == 1
+    inserted_rows: list[tuple[str, str, Any]] = citation_calls[0][0][1]
+
+    # Every edge hangs off the canonical paper.id (citing side).
+    assert all(row[0] == paper.id for row in inserted_rows)
+
+    cited_ids = {row[1] for row in inserted_rows}
+    assert cited_ids == {
+        "10.1007/s00454-019-00132-8",  # mixed-case → lower-cased
+        "10.1145/abc.123",  # URL prefix stripped + lower-cased
+        "10.1/mixedcase",  # doi: prefix stripped + lower-cased
+        "2101.00001",  # arXiv id untouched
+    }
+    # No raw URL-form / prefixed DOI leaked into the citation graph.
+    assert not any(cid.startswith(("http", "doi:")) for cid in cited_ids)
+
+
 # ---------------------------------------------------------------------------
 # 4. test_ingest_paper_not_found
 # ---------------------------------------------------------------------------
@@ -279,7 +418,7 @@ def test_ingest_paper_idempotent() -> None:
 
 
 def test_ingest_paper_arxiv_s2_fallback() -> None:
-    """If OpenAlex returns None for an arXiv ID, S2 fallback produces a stub Paper."""
+    """OpenAlex None + arXiv has nothing → stub Paper; S2 references still consulted."""
     paper_id = "2301.07041"
     mock_conn = MagicMock()
     mock_conn.execute = MagicMock()
@@ -288,17 +427,121 @@ def test_ingest_paper_arxiv_s2_fallback() -> None:
 
     with (
         patch("codex.ingest.openalex.fetch_paper", return_value=None),
+        # arXiv + abstract sources also empty → genuine stub fallback path.
+        patch("codex.ingest.arxiv.fetch_metadata", return_value=None) as mock_arxiv,
+        patch("codex.ingest.semanticscholar.fetch_abstract", return_value=None),
+        patch("codex.ingest.crossref.fetch_abstract", return_value=None),
         patch("codex.ingest.semanticscholar.fetch_references", return_value=[]) as mock_s2,
         patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
         patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
     ):
         result = ingest_paper(paper_id)
 
-    # S2 was consulted as fallback
+    # arXiv metadata recovery attempted; S2 references consulted as fallback.
+    mock_arxiv.assert_called_once_with(paper_id)
     mock_s2.assert_called()
     assert result.paper_id == paper_id
 
 
+def test_ingest_paper_openalex_404_recovers_from_arxiv() -> None:
+    """DQ-2: OpenAlex 404 on an arXiv id → authoritative metadata from the arXiv API,
+    bibkey auto-generated, abstract embedded (no zero vector)."""
+    recovered = Paper(
+        id="1911.00966",
+        title="A discrete version of Liouville's theorem on conformal maps",
+        authors=["Ulrich Pinkall", "Boris Springborn"],
+        year=2019,
+        abstract="Liouville's theorem says that in dimension greater than two...",
+    )
+    fake_emb = _fake_embedder()
+    mock_conn = MagicMock()
+    mock_conn.execute = MagicMock()
+    mock_conn.executemany = MagicMock()
+    mock_conn.commit = MagicMock()
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=None),
+        patch("codex.ingest.arxiv.fetch_metadata", return_value=recovered) as mock_arxiv,
+        patch("codex.ingest.semanticscholar.fetch_references", return_value=[]),
+        patch("codex.ingest.get_embedder", return_value=fake_emb),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        result = ingest_paper("1911.00966")
+
+    mock_arxiv.assert_called_once_with("1911.00966")
+    assert result.paper_id == "1911.00966"
+    params: dict[str, Any] = mock_conn.execute.call_args_list[0][0][1]
+    assert params["title"].startswith("A discrete version")
+    assert params["bibkey"] == "PinkallSpringborn2019"  # generated from recovered authors+year
+    # abstract present → real embedding computed, not a zero vector
+    fake_emb.encode_dense.assert_called_once()
+
+
+def test_ingest_paper_empty_abstract_recovered_from_s2() -> None:
+    """DQ-2: OpenAlex has the paper but no abstract → supplemented from S2 before embedding."""
+    paper = _make_paper(abstract=None)  # has openalex_id, no abstract
+    fake_emb = _fake_embedder()
+    mock_conn = MagicMock()
+    mock_conn.execute = MagicMock()
+    mock_conn.executemany = MagicMock()
+    mock_conn.commit = MagicMock()
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=paper),
+        patch("codex.ingest.openalex.fetch_citations", return_value=[]),
+        patch("codex.ingest.semanticscholar.fetch_references", return_value=[]),
+        patch(
+            "codex.ingest.semanticscholar.fetch_abstract",
+            return_value="Recovered abstract text.",
+        ) as mock_abs,
+        patch("codex.ingest.get_embedder", return_value=fake_emb),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        ingest_paper(paper.id)
+
+    mock_abs.assert_called_once()
+    params: dict[str, Any] = mock_conn.execute.call_args_list[0][0][1]
+    assert params["abstract"] == "Recovered abstract text."
+    fake_emb.encode_dense.assert_called_once_with(["Recovered abstract text."])
+
+
+def test_ingest_paper_openalex_empty_uses_s2_supplement() -> None:
+    """DQ-1: OpenAlex returns an empty reference list → ingest supplements from S2,
+    rewriting citing_id to paper.id and lowercasing DOI cited-ids."""
+    paper = _make_paper()  # openalex_id="W123", id="2301.07041"
+    mock_conn = MagicMock()
+    mock_conn.execute = MagicMock()
+    mock_conn.executemany = MagicMock()
+    mock_conn.commit = MagicMock()
+
+    # S2 keys citing_id by the id form passed in; ingest must canonicalise it.
+    s2_refs = [
+        Citation(citing_id="arXiv:2301.07041", cited_id="10.1/UPPER", context="ctx"),
+        Citation(citing_id="arXiv:2301.07041", cited_id="2202.00002"),
+    ]
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=paper),
+        patch("codex.ingest.openalex.fetch_citations", return_value=[]),
+        patch("codex.ingest.semanticscholar.fetch_references", return_value=s2_refs) as mock_s2,
+        patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        result = ingest_paper(paper.id)
+
+    # S2 consulted with a namespaced id (a bare arXiv id 404s on S2).
+    mock_s2.assert_called_once_with("arXiv:2301.07041")
+    assert result.citations_upserted == 2
+
+    mock_cursor = mock_conn.cursor.return_value.__enter__.return_value
+    inserted_rows: list[tuple[str, str, Any]] = mock_cursor.executemany.call_args_list[0][0][1]
+    # citing_id rewritten to paper.id, not the S2 id form.
+    assert all(row[0] == paper.id for row in inserted_rows)
+    cited = {row[1] for row in inserted_rows}
+    assert "10.1/upper" in cited  # DOI lowercased
+    assert "2202.00002" in cited  # arXiv id untouched
+
+
 # ---------------------------------------------------------------------------
 # 7. test_ingest_paper_no_abstract_uses_zero_vector
 # ---------------------------------------------------------------------------
@@ -317,6 +560,9 @@ def test_ingest_paper_no_abstract_uses_zero_vector() -> None:
     with (
         patch("codex.ingest.openalex.fetch_paper", return_value=paper),
         patch("codex.ingest.openalex.fetch_citations", return_value=[]),
+        # No abstract recoverable from any source (DQ-2) → genuine zero-vector case.
+        patch("codex.ingest.semanticscholar.fetch_abstract", return_value=None),
+        patch("codex.ingest.crossref.fetch_abstract", return_value=None),
         patch("codex.ingest.get_embedder", return_value=fake_emb),
         patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
     ):
@@ -526,6 +772,93 @@ def test_ingest_sets_bibkey_when_none(tmp_path: Any) -> None:
     assert upsert_params["bibkey"] == "AliceBob2023"
 
 
+def test_ingest_doi_paper_upserts_bare_canonical_id() -> None:
+    """DQ-5 regression: re-ingesting an existing DOI paper must be idempotent.
+
+    OpenAlex returns the ``doi`` as a full URL (and possibly mixed-case), but the
+    stored canonical ``papers.id`` is the BARE, lower-cased DOI (M-1 migration).
+    The papers upsert must therefore carry the BARE id into ``%(id)s`` so
+    ``ON CONFLICT (id)`` matches the existing row and UPDATEs it — rather than
+    attempting a fresh INSERT that trips the separate ``papers_openalex_id_key``
+    unique constraint (the UniqueViolation crash).
+
+    The real ``_map_paper``/``fetch_paper`` run here (only the HTTP ``_get``, the
+    embedder and the DB are mocked), so this exercises the actual normalization
+    through the ingest path. The DB is a MagicMock, so it cannot raise the real
+    constraint error; the live re-ingest of 10.1007/s00454-019-00132-8 is the
+    end-to-end UniqueViolation proof (see DATA-QUALITY-2026-06-15.md, DQ-5).
+    """
+    bare = "10.1007/s00454-019-00132-8"
+    work = {
+        "id": "https://openalex.org/W2899262408",
+        # URL form + an upper-case suffix char — the worst case for ON CONFLICT.
+        "doi": "https://doi.org/10.1007/S00454-019-00132-8",
+        "title": "A Test Paper",
+        "publication_year": 2019,
+        "authorships": [{"author": {"display_name": "Alice Smith"}}],
+        "abstract_inverted_index": {"Hello": [0], "world": [1]},
+        # Non-empty so fetch_citations yields edges and the S2 fallback is skipped.
+        "referenced_works": ["https://openalex.org/W1"],
+    }
+
+    mock_conn = MagicMock()
+    mock_conn.execute = MagicMock()
+    mock_conn.executemany = MagicMock()
+    mock_conn.commit = MagicMock()
+
+    with (
+        patch(
+            "codex.ingest.openalex._get",
+            return_value=httpx.Response(200, json=work),
+        ),
+        patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        result = ingest_paper(bare)
+
+    # The IngestResult and the upsert must use the bare canonical id, not the URL.
+    assert result.paper_id == bare
+
+    upsert_sql: str = mock_conn.execute.call_args_list[0][0][0]
+    upsert_params: dict[str, Any] = mock_conn.execute.call_args_list[0][0][1]
+    assert "INSERT INTO papers" in upsert_sql
+    assert "ON CONFLICT (id)" in upsert_sql
+    assert upsert_params["id"] == bare, (
+        f"upsert id must be the bare canonical DOI '{bare}', "
+        f"not the OpenAlex URL form '{upsert_params['id']}'"
+    )
+
+
+def test_ingest_normalizes_non_bare_caller_id() -> None:
+    """Review #1: a non-bare CALLER id (URL-form / mixed-case DOI) is normalized to the
+    bare canonical form before being pinned to papers.id (the C-7 pin runs it through
+    _norm_cited_id), so a sloppy caller cannot store a URL-form papers.id that would
+    defeat ON CONFLICT (id) idempotency or the ``paper.id.startswith('10.')`` gates."""
+    paper = _make_paper(paper_id="10.1007/s00454-019-00132-8", openalex_id="W1")
+    mock_conn = MagicMock()
+    mock_conn.execute = MagicMock()
+    mock_conn.executemany = MagicMock()
+    mock_conn.commit = MagicMock()
+
+    with (
+        patch("codex.ingest.openalex.fetch_paper", return_value=paper),
+        patch("codex.ingest.openalex.fetch_citations", return_value=[]),
+        patch("codex.ingest.semanticscholar.fetch_references", return_value=[]),
+        patch("codex.ingest.crossref.fetch_references", return_value=[]),
+        patch("codex.ingest.get_embedder", return_value=_fake_embedder()),
+        patch("codex.ingest.get_conn", side_effect=_make_conn_cm(mock_conn)),
+    ):
+        # Caller passes the URL form with an upper-case suffix char (worst case).
+        result = ingest_paper("https://doi.org/10.1007/S00454-019-00132-8")
+
+    bare = "10.1007/s00454-019-00132-8"
+    assert result.paper_id == bare
+    upsert_params: dict[str, Any] = mock_conn.execute.call_args_list[0][0][1]
+    assert upsert_params["id"] == bare, (
+        f"non-bare caller must be normalized to '{bare}', got '{upsert_params['id']}'"
+    )
+
+
 def test_ingest_disambiguates_bibkey_on_unique_violation() -> None:
     """A papers.bibkey UNIQUE collision is retried with an a/b/c suffix (audit C-15)."""
     paper = _make_paper()  # bibkey auto-generates to "AliceBob2023"

tests/parsing/test_tex.py

@@ -4,7 +4,13 @@ from __future__ import annotations
 
 import pytest
 
-from codex.parsing.tex import chunk_text, extract_sections, latex_to_text
+from codex.parsing.tex import (
+    chunk_sections,
+    chunk_text,
+    extract_sections,
+    flatten_inputs,
+    latex_to_text,
+)
 
 
 class TestExtractSections:
@@ -110,3 +116,62 @@ class TestLatexToText:
         result = latex_to_text(latex)
         assert r"\cite" not in result
         assert "%" not in result
+
+
+class TestFlattenInputs:
+    def test_inlines_input_and_include(self) -> None:
+        files = {
+            "main.tex": r"Start \input{sec/intro} mid \include{proof} end",
+            "sec/intro.tex": "INTRO BODY",
+            "proof.tex": "PROOF BODY",
+        }
+        out = flatten_inputs(files["main.tex"], files)
+        assert "INTRO BODY" in out
+        assert "PROOF BODY" in out
+        assert r"\input" not in out and r"\include" not in out
+
+    def test_resolves_without_tex_suffix(self) -> None:
+        # \input{intro} must resolve the archive member "intro.tex".
+        files = {"main.tex": r"\input{intro}", "intro.tex": "BODY"}
+        assert "BODY" in flatten_inputs(files["main.tex"], files)
+
+    def test_recursive_includes(self) -> None:
+        files = {"a.tex": r"X \input{b}", "b.tex": r"Y \input{c}", "c.tex": "Z"}
+        out = flatten_inputs(files["a.tex"], files)
+        assert "X" in out and "Y" in out and "Z" in out
+
+    def test_unresolved_input_dropped(self) -> None:
+        # A reference with no matching file is removed, not left as a directive.
+        out = flatten_inputs(r"A \input{missing} B", {})
+        assert r"\input" not in out
+        assert "A" in out and "B" in out
+
+    def test_input_cycle_does_not_leak_directive(self) -> None:
+        # a -> b -> a: the depth cap must strip the unresolved directive, not leak it.
+        files = {"a.tex": r"AA \input{b}", "b.tex": r"BB \input{a}"}
+        out = flatten_inputs(files["a.tex"], files)
+        assert r"\input" not in out
+        assert "AA" in out and "BB" in out
+
+    def test_dot_slash_prefix_resolves_without_overstrip(self) -> None:
+        # "./intro" resolves intro.tex; lstrip must not eat a real leading dot/run.
+        files = {"main.tex": r"\input{./intro}", "intro.tex": "BODY"}
+        assert "BODY" in flatten_inputs(files["main.tex"], files)
+
+
+class TestChunkSections:
+    def test_pairs_carry_section_titles(self) -> None:
+        latex = (
+            r"\section{Introduction}" + "\nIntro body text here.\n"
+            r"\section{Proof}" + "\nProof body text here.\n"
+        )
+        pairs = chunk_sections(latex)
+        titles = [t for t, _ in pairs]
+        assert "Introduction" in titles
+        assert "Proof" in titles
+        # No chunk spans a section boundary: each chunk belongs to one title.
+        assert all(isinstance(c, str) and c for _, c in pairs)
+
+    def test_fallback_titleless_when_no_sections(self) -> None:
+        pairs = chunk_sections("Plain text with no section commands at all here.")
+        assert pairs and all(title is None for title, _ in pairs)

tests/quality/test_quality.py

@@ -6,10 +6,12 @@ from unittest.mock import MagicMock
 
 from codex.quality import (
     _bib_score,
+    _clean_title,
     classify_section,
     filter_chunks,
     is_quality_chunk,
     run_quality_pass,
+    section_label,
 )
 
 # ---------------------------------------------------------------------------
@@ -243,3 +245,58 @@ class TestRunQualityPass:
         kwargs = update_calls[0][0][1]
         assert kwargs["section"] == "abstract"
         assert kwargs["id"] == 5
+
+
+class TestCleanTitle:
+    def test_strips_leading_numbering(self):
+        assert _clean_title("3.2 Variational Principles") == "variational principles"
+
+    def test_strips_latex_and_braces(self):
+        assert _clean_title(r"The \emph{Discrete} Laplacian") == "the discrete laplacian"
+
+    def test_collapses_and_lowercases(self):
+        assert _clean_title("  Rigidity   Results  ") == "rigidity results"
+
+    def test_strips_accent_macros(self):
+        assert _clean_title(r"M\"obius Invariance") == "mobius invariance"
+
+    def test_strips_ties_and_accents(self):
+        assert _clean_title(r"Colin~de~Verdi\`ere") == "colin de verdiere"
+
+    def test_truncates_at_word_boundary(self):
+        long = "alpha beta gamma delta epsilon zeta eta theta iota kappa lambda mu nu omega"
+        out = _clean_title(long)
+        assert len(out) <= 60
+        assert not out.endswith(" ")
+        assert long.lower().startswith(out)  # whole words from the start, no partial tail
+
+
+class TestSectionLabel:
+    def test_bare_canonical_heading_maps_to_bucket(self):
+        # Only an EXACT canonical heading collapses to its controlled bucket.
+        assert section_label("Introduction", "body text") == "intro"
+        assert section_label("Proof", "body text") == "proof"
+        assert section_label("References", "body text") == "bibliography"
+        assert section_label("Abstract", "body text") == "abstract"
+
+    def test_descriptive_title_stored_verbatim(self):
+        # R-F: a heading that merely STARTS with a keyword keeps its real title,
+        # not the bucket — fixes classify_section prefix-match over-bucketing.
+        assert section_label("Preliminaries", "body text") == "preliminaries"
+        assert section_label("3.1 Discrete Conformal Maps", "x") == "discrete conformal maps"
+        assert section_label("Proof of Theorem 3", "x") == "proof of theorem 3"
+        assert section_label("Abstract Nonsense and Categories", "x") == (
+            "abstract nonsense and categories"
+        )
+        assert section_label("Introduction to Operator Algebras", "x") == (
+            "introduction to operator algebras"
+        )
+
+    def test_none_or_blank_title_falls_back_to_content(self):
+        # .pdf/.txt path: unchanged content-based classification.
+        assert section_label(None, "Theorem 1. Let X be ...") == "theorem"
+        assert section_label("", "ordinary body prose here") == "body"
+
+    def test_title_cleaning_to_empty_falls_back_to_content(self):
+        # A pure-numbering heading cleans to "" → classify by content instead.
+        assert section_label("3.2", "Lemma 2. Suppose ...") == "theorem"

tests/scripts/test_ra_grobid_backfill.py

@@ -0,0 +1,112 @@
+"""Tests for scripts.ra_grobid_backfill — the R-A GROBID references backfill.
+
+Only the pure, offline logic is covered (id normalization + Citation assembly);
+``extract_references`` is mocked so no GROBID server or DB is required.
+"""
+
+from __future__ import annotations
+
+from contextlib import contextmanager
+from typing import Any
+from unittest.mock import MagicMock, patch
+
+from codex.models import Citation
+from scripts.ra_grobid_backfill import _normalize_cited_id, build_grobid_citations, main
+
+# ---------------------------------------------------------------------------
+# _normalize_cited_id
+# ---------------------------------------------------------------------------
+
+
+def test_normalize_doi_url_to_bare_lowercase() -> None:
+    assert _normalize_cited_id(doi="https://doi.org/10.1007/S00454-019-00132-8") == (
+        "10.1007/s00454-019-00132-8"
+    )
+
+
+def test_normalize_doi_prefixes() -> None:
+    assert _normalize_cited_id(doi="http://doi.org/10.1/X") == "10.1/x"
+    assert _normalize_cited_id(doi="doi:10.1/X") == "10.1/x"
+    assert _normalize_cited_id(doi="10.1/x") == "10.1/x"
+
+
+def test_normalize_arxiv_prefix_stripped() -> None:
+    assert _normalize_cited_id(arxiv_id="arXiv:2305.10988") == "2305.10988"
+    assert _normalize_cited_id(arxiv_id="2305.10988") == "2305.10988"
+    # Legacy ids keep their slash.
+    assert _normalize_cited_id(arxiv_id="math/0603097") == "math/0603097"
+
+
+def test_normalize_doi_takes_precedence_over_arxiv() -> None:
+    assert _normalize_cited_id(doi="10.5/y", arxiv_id="2305.10988") == "10.5/y"
+
+
+def test_normalize_empty_returns_none() -> None:
+    assert _normalize_cited_id() is None
+    assert _normalize_cited_id(doi="   ", arxiv_id="") is None
+
+
+# ---------------------------------------------------------------------------
+# build_grobid_citations
+# ---------------------------------------------------------------------------
+
+
+def _ref(doi: str = "", arxiv_id: str = "") -> dict[str, str]:
+    return {"title": "t", "authors": "a", "year": "2020", "doi": doi, "arxiv_id": arxiv_id}
+
+
+def test_build_citations_normalizes_dedups_and_drops_self() -> None:
+    paper_id = "10.1007/s00454-019-00132-8"
+    refs = [
+        _ref(doi="https://doi.org/10.1/A"),  # → 10.1/a
+        _ref(doi="DOI:10.1/a"),  # duplicate of the above after normalization
+        _ref(arxiv_id="arXiv:2305.10988"),  # → 2305.10988
+        _ref(doi="", arxiv_id=""),  # no id → skipped
+        _ref(doi="https://doi.org/10.1007/S00454-019-00132-8"),  # self-cite → dropped
+    ]
+    with patch("scripts.ra_grobid_backfill.extract_references", return_value=refs) as mock_ex:
+        cits = build_grobid_citations(paper_id, "some.pdf", grobid_url="http://grobid")
+
+    mock_ex.assert_called_once_with("some.pdf", grobid_url="http://grobid", timeout=60.0)
+    assert all(isinstance(c, Citation) for c in cits)
+    assert all(c.citing_id == paper_id for c in cits)
+    assert [c.cited_id for c in cits] == ["10.1/a", "2305.10988"]
+
+
+def test_build_citations_empty_when_no_refs() -> None:
+    with patch("scripts.ra_grobid_backfill.extract_references", return_value=[]):
+        assert build_grobid_citations("10.1/x", "x.pdf") == []
+
+
+# ---------------------------------------------------------------------------
+# main — connection scope (review finding #4)
+# ---------------------------------------------------------------------------
+
+
+def test_main_uses_separate_connections_for_read_and_write(tmp_path: Any) -> None:
+    """Review #4: the read connection is released BEFORE the slow GROBID loop, and a
+    fresh connection is opened for the write — so no idle-in-transaction connection
+    spans the per-paper network loop (which would abort on an SSH-tunnel drop)."""
+    (tmp_path / "paper.pdf").write_bytes(b"%PDF-1.4")
+    conns: list[MagicMock] = []
+
+    @contextmanager
+    def fake_get_conn() -> Any:
+        c = MagicMock()
+        c.execute.return_value.fetchall.return_value = [
+            {"id": "10.1/x", "source_path": "/d/paper.txt", "out_edges": 0}
+        ]
+        c.execute.return_value.fetchone.return_value = {"papers": 1, "citing": 1, "edges": 1}
+        conns.append(c)
+        yield c
+
+    with (
+        patch("scripts.ra_grobid_backfill.get_conn", side_effect=fake_get_conn),
+        patch("scripts.ra_grobid_backfill.build_grobid_citations", return_value=[]),
+    ):
+        rc = main(["--pdf-dir", str(tmp_path), "--write"])
+
+    assert rc == 0
+    # Two DISTINCT get_conn() context managers (read, then write) — not one held
+    # open across the GROBID loop.
+    assert len(conns) == 2

tests/scripts/test_rc_tex_reingest.py

@@ -0,0 +1,21 @@
+"""Tests for scripts.rc_tex_reingest."""
+
+from __future__ import annotations
+
+from scripts.rc_tex_reingest import is_arxiv_id
+
+
+def test_is_arxiv_id_accepts_modern_and_legacy() -> None:
+    assert is_arxiv_id("2305.10988")
+    assert is_arxiv_id("math/0603097")
+    assert is_arxiv_id("1005.2698")
+
+
+def test_is_arxiv_id_rejects_dois_and_wids() -> None:
+    assert not is_arxiv_id("10.1007/s00454-019-00132-8")
+    assert not is_arxiv_id("10.14279/depositonce-20357")
+    assert not is_arxiv_id("W2971636899")
+    assert not is_arxiv_id("https://openalex.org/W2971636899")
+    assert not is_arxiv_id("http://openalex.org/W2971636899")
+    assert not is_arxiv_id("10.48550/arXiv.2305.10988")  # arXiv DOI form, not bare id
+    assert not is_arxiv_id("")

tests/sources/test_arxiv.py

@@ -53,6 +53,94 @@ def test_fetch_source_returns_latex(monkeypatch: pytest.MonkeyPatch) -> None:
     assert "Hello world" in result
 
 
+def test_fetch_source_flattens_multifile(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Multi-file projects: \\input/\\include directives are inlined so the body
+    from the included files is returned, not just the primary skeleton (R-C)."""
+    main = (
+        b"\\documentclass{article}\\begin{document}"
+        b"\\input{sections/intro}\\include{proof}\\end{document}"
+    )
+    tar_bytes = _make_tar_gz(
+        {
+            "main.tex": main,
+            "sections/intro.tex": b"INTRODUCTION BODY TEXT",
+            "proof.tex": b"PROOF BODY TEXT",
+        }
+    )
+
+    def mock_get(
+        url: str,
+        *,
+        timeout: int = 60,
+        follow_redirects: bool = True,
+    ) -> httpx.Response:
+        return httpx.Response(200, content=tar_bytes)
+
+    monkeypatch.setattr(httpx, "get", mock_get)
+
+    result = arxiv.fetch_source("2301.07041")
+
+    assert result is not None
+    assert "INTRODUCTION BODY TEXT" in result  # \input was inlined
+    assert "PROOF BODY TEXT" in result  # \include was inlined
+    assert "\\input" not in result and "\\include" not in result
+
+
+def test_fetch_source_bare_gzip_single_file(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Legacy arXiv submissions are served as a single bare gzipped .tex (no tar
+    wrapper); fetch_source must gunzip the body directly rather than fail."""
+    import gzip
+
+    latex = b"\\documentstyle[a4]{article}\n\\section{Intro}\nOld single-file paper body."
+    gz_bytes = gzip.compress(latex)
+
+    def mock_get(
+        url: str,
+        *,
+        timeout: int = 60,
+        follow_redirects: bool = True,
+    ) -> httpx.Response:
+        return httpx.Response(200, content=gz_bytes)
+
+    monkeypatch.setattr(httpx, "get", mock_get)
+
+    result = arxiv.fetch_source("math/0001176")
+
+    assert result is not None
+    assert "Old single-file paper body." in result
+
+
+def test_fetch_source_resolves_non_tex_include(monkeypatch: pytest.MonkeyPatch) -> None:
+    """\\input of a non-.tex body member (e.g. a .def file) is inlined, not dropped (R-C)."""
+    main = b"\\documentclass{article}\\begin{document}\\input{body.def}\\end{document}"
+    tar_bytes = _make_tar_gz({"main.tex": main, "body.def": b"NON TEX BODY TEXT"})
+
+    def mock_get(url: str, *, timeout: int = 60, follow_redirects: bool = True) -> httpx.Response:
+        return httpx.Response(200, content=tar_bytes)
+
+    monkeypatch.setattr(httpx, "get", mock_get)
+    result = arxiv.fetch_source("2301.07041")
+    assert result is not None
+    assert "NON TEX BODY TEXT" in result
+
+
+def test_fetch_source_ignores_commented_documentclass(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A commented %\\documentclass must not select a file as the primary document."""
+    decoy = b"% \\documentclass{article}\n\\section{Stub}\nDECOY ONLY"
+    real = b"\\documentclass{book}\\begin{document}REAL BODY HERE\\end{document}"
+    # decoy sorts/inserts first; without the fix it would win on the substring match.
+    tar_bytes = _make_tar_gz({"aaa_decoy.tex": decoy, "real.tex": real})
+
+    def mock_get(url: str, *, timeout: int = 60, follow_redirects: bool = True) -> httpx.Response:
+        return httpx.Response(200, content=tar_bytes)
+
+    monkeypatch.setattr(httpx, "get", mock_get)
+    result = arxiv.fetch_source("2301.07041")
+    assert result is not None
+    assert "REAL BODY HERE" in result
+    assert "DECOY ONLY" not in result
+
+
 # ---------------------------------------------------------------------------
 # fetch_source — 404 → None
 # ---------------------------------------------------------------------------
@@ -138,3 +226,63 @@ def test_fetch_pdf_url_pure_computation() -> None:
 
     url2 = arxiv.fetch_pdf_url("1234.56789")
     assert url2 == "https://arxiv.org/pdf/1234.56789.pdf"
+
+
+# ---------------------------------------------------------------------------
+# fetch_metadata — parse the Atom feed into a Paper (DQ-2)
+# ---------------------------------------------------------------------------
+
+_ATOM_FEED = """<?xml version="1.0" encoding="UTF-8"?>
+<feed xmlns="http://www.w3.org/2005/Atom">
+  <entry>
+    <title>A discrete version of Liouville's theorem on conformal maps</title>
+    <summary>Liouville's theorem says that in dimension greater than two,
+    all conformal maps are Moebius transformations.</summary>
+    <published>2019-11-03T00:00:00Z</published>
+    <author><name>Ulrich Pinkall</name></author>
+    <author><name>Boris Springborn</name></author>
+  </entry>
+</feed>"""
+
+_ATOM_EMPTY = """<?xml version="1.0" encoding="UTF-8"?>
+<feed xmlns="http://www.w3.org/2005/Atom"><title>ArXiv Query</title></feed>"""
+
+
+def test_fetch_metadata_parses_entry(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A valid Atom feed yields a populated Paper."""
+
+    def mock_get(url: str, **kwargs: object) -> httpx.Response:
+        return httpx.Response(200, text=_ATOM_FEED, request=httpx.Request("GET", url))
+
+    monkeypatch.setattr(httpx, "get", mock_get)
+
+    paper = arxiv.fetch_metadata("1911.00966")
+    assert paper is not None
+    assert paper.id == "1911.00966"
+    assert paper.title.startswith("A discrete version of Liouville")
+    assert paper.authors == ["Ulrich Pinkall", "Boris Springborn"]
+    assert paper.year == 2019
+    assert paper.abstract and "conformal maps" in paper.abstract
+    assert paper.openalex_id is None
+
+
+def test_fetch_metadata_no_entry_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A feed with no <entry> (id not found) returns None."""
+
+    def mock_get(url: str, **kwargs: object) -> httpx.Response:
+        return httpx.Response(200, text=_ATOM_EMPTY, request=httpx.Request("GET", url))
+
+    monkeypatch.setattr(httpx, "get", mock_get)
+    assert arxiv.fetch_metadata("0000.00000") is None
+
+
+def test_fetch_metadata_strips_arxiv_prefix(monkeypatch: pytest.MonkeyPatch) -> None:
+    """An ``arXiv:`` prefix is stripped so Paper.id is the bare id."""
+
+    def mock_get(url: str, **kwargs: object) -> httpx.Response:
+        return httpx.Response(200, text=_ATOM_FEED, request=httpx.Request("GET", url))
+
+    monkeypatch.setattr(httpx, "get", mock_get)
+    paper = arxiv.fetch_metadata("arXiv:1911.00966")
+    assert paper is not None
+    assert paper.id == "1911.00966"

tests/sources/test_crossref.py

@@ -0,0 +1,104 @@
+"""Tests for codex.sources.crossref."""
+
+from __future__ import annotations
+
+import httpx
+import pytest
+
+from codex.models import Citation
+from codex.sources import crossref
+
+
+def test_fetch_abstract_strips_jats(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A JATS-tagged abstract is returned as plain text with tags removed."""
+    body = {
+        "message": {
+            "abstract": "<jats:p>We prove a <jats:italic>theorem</jats:italic> about "
+            "polyhedra.</jats:p>"
+        }
+    }
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        return httpx.Response(200, json=body)
+
+    monkeypatch.setattr(crossref, "_get", mock_get)
+
+    result = crossref.fetch_abstract("10.1007/s00454-019-00132-8")
+    assert result == "We prove a theorem about polyhedra."
+
+
+def test_fetch_abstract_absent_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A work with no abstract field (e.g. a book chapter) returns None."""
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        return httpx.Response(200, json={"message": {"title": ["Some Chapter"]}})
+
+    monkeypatch.setattr(crossref, "_get", mock_get)
+    assert crossref.fetch_abstract("10.1007/978-3-642-17413-1_7") is None
+
+
+def test_fetch_abstract_404_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A 404 returns None rather than raising."""
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        raise httpx.HTTPStatusError(
+            "404",
+            request=httpx.Request("GET", url),
+            response=httpx.Response(404, request=httpx.Request("GET", url)),
+        )
+
+    monkeypatch.setattr(crossref, "_get", mock_get)
+    assert crossref.fetch_abstract("10.0000/nonexistent") is None
+
+
+# ---------------------------------------------------------------------------
+# fetch_references (roadmap R-B)
+# ---------------------------------------------------------------------------
+
+
+def test_fetch_references_returns_doi_edges(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Only references carrying a DOI become Citations; citing_id is the queried DOI."""
+    body = {
+        "message": {
+            "reference": [
+                {"key": "ref1", "DOI": "10.1090/s0002-9947-04-03545-7"},
+                {"key": "ref2", "unstructured": "A book with no DOI, 1992."},  # skipped
+                {"key": "ref3", "DOI": "10.1007/bf02392449", "article-title": "X"},
+            ]
+        }
+    }
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        return httpx.Response(200, json=body)
+
+    monkeypatch.setattr(crossref, "_get", mock_get)
+    refs = crossref.fetch_references("10.1007/s00454-019-00132-8")
+
+    assert refs == [
+        Citation(citing_id="10.1007/s00454-019-00132-8", cited_id="10.1090/s0002-9947-04-03545-7"),
+        Citation(citing_id="10.1007/s00454-019-00132-8", cited_id="10.1007/bf02392449"),
+    ]
+
+
+def test_fetch_references_no_reference_key_returns_empty(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A work with no deposited reference list returns []."""
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        return httpx.Response(200, json={"message": {"title": ["No refs deposited"]}})
+
+    monkeypatch.setattr(crossref, "_get", mock_get)
+    assert crossref.fetch_references("10.1007/978-3-642-17413-1_7") == []
+
+
+def test_fetch_references_404_returns_empty(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A 404 returns [] rather than raising."""
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        raise httpx.HTTPStatusError(
+            "404",
+            request=httpx.Request("GET", url),
+            response=httpx.Response(404, request=httpx.Request("GET", url)),
+        )
+
+    monkeypatch.setattr(crossref, "_get", mock_get)
+    assert crossref.fetch_references("10.0000/nonexistent") == []

tests/sources/test_openalex.py

@@ -7,7 +7,7 @@ import pytest
 
 from codex.models import Citation, Paper
 from codex.sources import openalex
-from codex.sources.openalex import _resolve_id
+from codex.sources.openalex import _canonical_id, _normalize_doi, _resolve_id
 
 # ---------------------------------------------------------------------------
 # Helpers
@@ -15,7 +15,8 @@ from codex.sources.openalex import _resolve_id
 
 _SAMPLE_WORK = {
     "id": "https://openalex.org/W2741809807",
-    # Real OpenAlex returns the DOI as a full URL, not a bare DOI (audit T-3).
+    # Real OpenAlex returns the DOI as a full URL, not a bare DOI (audit T-3 / DQ-5
+    # — the old bare fixture hid the URL-form behaviour both fixes address).
     "doi": "https://doi.org/10.1145/3592430",
     "title": "Conformal Prediction: A Review",
     "publication_year": 2023,
@@ -68,6 +69,87 @@ def test_resolve_prefixed_unchanged() -> None:
     assert _resolve_id("doi:10.1145/x") == "doi:10.1145/x"
 
 
+# ---------------------------------------------------------------------------
+# _normalize_doi — canonical bare, lower-cased form (DQ-5)
+# ---------------------------------------------------------------------------
+
+
+def test_normalize_doi_strips_https_url() -> None:
+    # The exact form OpenAlex returns in the `doi` field.
+    assert _normalize_doi("https://doi.org/10.1007/s00454-019-00132-8") == (
+        "10.1007/s00454-019-00132-8"
+    )
+
+
+def test_normalize_doi_strips_http_and_doi_prefix() -> None:
+    assert _normalize_doi("http://doi.org/10.1145/3592430") == "10.1145/3592430"
+    assert _normalize_doi("doi:10.1145/3592430") == "10.1145/3592430"
+
+
+def test_normalize_doi_lowercases() -> None:
+    # DOIs are case-insensitive; the canonical id (and _norm_cited_id) is lower-case.
+    assert _normalize_doi("https://doi.org/10.1007/S00454-019-00132-8") == (
+        "10.1007/s00454-019-00132-8"
+    )
+
+
+def test_normalize_doi_already_bare_is_idempotent() -> None:
+    assert _normalize_doi("10.1007/s00454-019-00132-8") == "10.1007/s00454-019-00132-8"
+
+
+# ---------------------------------------------------------------------------
+# _canonical_id — arXiv DOI → bare arXiv id (arXiv half of DQ-5)
+# ---------------------------------------------------------------------------
+
+
+def test_canonical_id_strips_arxiv_doi_modern() -> None:
+    # arXiv works carry the arXiv DOI; the canonical id is the bare arXiv id.
+    assert _canonical_id("https://doi.org/10.48550/arXiv.2305.10988") == "2305.10988"
+
+
+def test_canonical_id_strips_arxiv_doi_legacy() -> None:
+    assert _canonical_id("https://doi.org/10.48550/arXiv.math/0603097") == "math/0603097"
+
+
+def test_canonical_id_leaves_regular_doi_bare() -> None:
+    # A normal journal DOI is only normalized (bare + lower-case), not stripped.
+    assert _canonical_id("https://doi.org/10.1007/S00454-019-00132-8") == (
+        "10.1007/s00454-019-00132-8"
+    )
+
+
+def test_fetch_paper_arxiv_doi_yields_bare_id(monkeypatch: pytest.MonkeyPatch) -> None:
+    """An arXiv work maps to the BARE arXiv id (not the arXiv DOI), so re-ingesting
+    by arXiv id hits ON CONFLICT (id) instead of tripping papers_openalex_id_key."""
+    work = {**_SAMPLE_WORK, "doi": "https://doi.org/10.48550/arXiv.2305.10988"}
+
+    def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
+        return httpx.Response(200, json=work)
+
+    monkeypatch.setattr(openalex, "_get", mock_get)
+    paper = openalex.fetch_paper("2305.10988")
+
+    assert paper is not None
+    assert paper.id == "2305.10988"
+
+
+def test_map_paper_falls_back_to_openalex_id_without_doi(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """A work with no DOI keeps the OpenAlex W-id (URL form) as id, unchanged —
+    normalization only rewrites the DOI branch."""
+    work = {k: v for k, v in _SAMPLE_WORK.items() if k != "doi"}
+
+    def mock_get(url: str, params: dict[str, str] | None = None) -> httpx.Response:
+        return httpx.Response(200, json=work)
+
+    monkeypatch.setattr(openalex, "_get", mock_get)
+    paper = openalex.fetch_paper("W2741809807")
+
+    assert paper is not None
+    assert paper.id == "https://openalex.org/W2741809807"
+
+
 # ---------------------------------------------------------------------------
 # fetch_paper — success
 # ---------------------------------------------------------------------------
@@ -86,15 +168,17 @@ def test_fetch_paper_success(monkeypatch: pytest.MonkeyPatch) -> None:
 
     assert paper is not None
     assert isinstance(paper, Paper)
+    # DQ-5: openalex._canonical_id normalizes OpenAlex's URL-form doi to the BARE
+    # lower-cased DOI at the source layer; ingest additionally pins papers.id to the
+    # caller's id (audit C-7). Both converge on the bare canonical id — which is what
+    # makes the ingest ON CONFLICT (id) upsert idempotent. (T-3: the fixture is
+    # URL-form so this mapping can't silently regress.)
+    assert paper.id == "10.1145/3592430"
     assert paper.title == "Conformal Prediction: A Review"
     assert paper.year == 2023
     assert paper.authors == ["Alice Smith", "Bob Jones"]
     assert paper.abstract == "Conformal prediction is great"
     assert paper.openalex_id == "https://openalex.org/W2741809807"
-    # fetch_paper maps id from the (URL-form) doi; ingest later canonicalises
-    # papers.id to the caller's bare id (audit C-7). Pin the real mapping here so
-    # the fixture cannot silently misrepresent OpenAlex again (audit T-3).
-    assert paper.id == "https://doi.org/10.1145/3592430"
 
 
 def test_fetch_paper_arxiv_id_prefixed(monkeypatch: pytest.MonkeyPatch) -> None:

tests/sources/test_semanticscholar.py

@@ -124,3 +124,46 @@ def test_fetch_recommendations_404_returns_empty(
 
     result = semanticscholar.fetch_recommendations("nonexistent")
     assert result == []
+
+
+# ---------------------------------------------------------------------------
+# fetch_references — {"data": null} guard (DQ-1 regression)
+# ---------------------------------------------------------------------------
+
+
+def test_fetch_references_null_data_returns_empty(monkeypatch: pytest.MonkeyPatch) -> None:
+    """S2 returns HTTP 200 with ``{"data": null}`` for a known paper that has no
+    parsed references; this must yield [] rather than raising TypeError."""
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        return httpx.Response(200, json={"data": None, "citingPaperInfo": {}})
+
+    monkeypatch.setattr(semanticscholar, "_get", mock_get)
+    assert semanticscholar.fetch_references("DOI:10.14279/depositonce-5415") == []
+
+
+# ---------------------------------------------------------------------------
+# fetch_abstract (DQ-2)
+# ---------------------------------------------------------------------------
+
+
+def test_fetch_abstract_returns_text(monkeypatch: pytest.MonkeyPatch) -> None:
+    """fetch_abstract returns the abstract string when present."""
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        return httpx.Response(200, json={"abstract": "We study ideal hyperbolic polyhedra."})
+
+    monkeypatch.setattr(semanticscholar, "_get", mock_get)
+    assert semanticscholar.fetch_abstract("DOI:10.1007/s00454-019-00132-8") == (
+        "We study ideal hyperbolic polyhedra."
+    )
+
+
+def test_fetch_abstract_null_returns_none(monkeypatch: pytest.MonkeyPatch) -> None:
+    """A null/absent abstract yields None."""
+
+    def mock_get(url: str, params: dict[str, object] | None = None) -> httpx.Response:
+        return httpx.Response(200, json={"abstract": None})
+
+    monkeypatch.setattr(semanticscholar, "_get", mock_get)
+    assert semanticscholar.fetch_abstract("arXiv:1234.5678") is None