Citation audit

Citation Audit

Core Rule

The bibliography is deterministic infrastructure: a \cite either resolves or it does not; a DOI is either well-formed or it is not. Per CLAUDE.md → Model vs Code, do not eyeball what a parser can decide. This skill is the deeper manual audit that complements the live hook — it catches the structural problems the gate does not (orphans, duplicates, malformed metadata, formatting drift) and reasons about fixes.

For the live \cite↔.bib and \ref↔\label check, the citation-gate.sh hook already runs after every .tex/.bib edit and writes its verdict to .hook-state/last_quality_gate.json. Tell the user to rely on that hook for continuous coverage; run /citation-audit for a thorough sweep before submission or when inheriting a messy .bib.

Never fix a dangling key by inventing a reference. A \cite{key} with no entry is resolved either by supplying verified metadata or by flagging [CITE] in the prose and removing the dead key — never by writing a plausible stub. block-fabrication.sh will block the stub anyway.

When to Use

Invoke with /citation-audit when:

• Preparing to submit — a clean bibliography is a Reviewer 2 freebie you should not give away.
• You merged a co-author's .bib and suspect duplicates or format drift.
• The citation-gate verdict shows dangling keys and you want the full structural picture, not just the first 25.
• Switching reference styles (ACS ↔ IEEE ↔ APA) and need to audit field completeness first.

Process

Phase 1: Inventory

Locate the manuscript root (nearest ancestor with a .bib, main.tex, or MANUSCRIPT_MAP.md) and inventory:

1. All .bib files — there may be more than one; the gate scans all of them.
2. All .tex/.ltx files — the sources of \cite and \ref.
3. Reference style in force — from MANUSCRIPT_MAP.md → Target journal (ACS / IEEE / APA / Nature). This sets which fields are required and the expected author/journal format.

Strip TeX comments before counting: a commented-out % \cite{foo} is not a real citation. (The gate does this; match its behaviour.)

Phase 2: Resolution Integrity (\cite ↔ .bib)

The same check the hook runs, surfaced in full:

1. Defined keys — parse @type{key, from every .bib (skip @string/@comment/@preamble).
2. Cited keys — parse the full \cite family from every .tex: \cite \citep \citet \citeauthor \autocite \textcite \parencite \footcite and friends, including multi-key braces {a,b,c} and optional [..] arguments.
3. Dangling cites — cited but not defined → ERROR. Each is a fabrication risk: resolve with verified metadata or flag [CITE] and remove the key. Do NOT invent the entry.
4. Orphan entries — defined but never cited → WARNING. Dead weight; remove unless deliberately retained (e.g. a \nocite{*} data-availability list — note the exception).

Phase 3: Duplicate Detection

Duplicates produce double-counted references and inconsistent keys:

1. Same key twice — a hard .bib error; biber/bibtex picks one silently. ERROR.
2. Same work, different keys — match on DOI, then on (normalized title + year + first author). Two keys for one paper means the manuscript cites it inconsistently. WARNING — merge to one key and update all \cite sites.
3. Near-duplicate titles — preprint vs published version of the same work. Flag for the author to pick the citeable version.

Phase 4: DOI and Identifier Validity

1. Placeholder / fake-shaped DOIs — 10.xxxx, 10.0000, 10.nnnn, example.com, your-doi, TODO → ERROR. (block-fabrication.sh blocks these on write; catch any that predate the hook.) Flag, never "complete" them.
2. Malformed DOIs — must match 10.<registrant>/<suffix>. A DOI that is not shaped like one is suspect.
3. arXiv / ISSN shape — sanity-check format. Do not assert a DOI "resolves" unless you verified it against a real source — shape validity is not existence.

Phase 5: Required-Field Completeness (per entry type)

Each @type has required fields; a missing one is a malformed reference. Check against the style in force:

Entry type	Required (BibTeX core)
@article	author, title, journal, year, (volume)
@book	author/editor, title, publisher, year
@incollection	author, title, booktitle, publisher, year
@inproceedings	author, title, booktitle, year
@phdthesis	author, title, school, year
@techreport	author, title, institution, year
@misc	title + (howpublished/url/year) for datasets, software, preprints

An empty required field (author = {}) is a stub masquerading as real → ERROR (the hook blocks writing these). A missing required field → WARNING. Supply the value only from the actual source.

Phase 6: Formatting Consistency

Drift here is what a copy-editor (and Reviewer 2) flags:

1. Author name format — one convention throughout (Last, First vs First Last; initials with/without periods; and separators). List the outliers.
2. Journal names — full vs abbreviated, consistently. ACS/IEEE expect ISO-4 abbreviations; APA/Nature expect full titles. Match the style.
3. Title case — sentence case vs title case per style; brace-protection on proper nouns/acronyms ({LLM}, {API}) so they aren't down-cased.
4. Page ranges — -- en-dash, consistent.
5. Capitalization protection — model names, acronyms, proper nouns wrapped in {}.

Do not silently rewrite all of these — reference style conversion is a deterministic job for a CSL processor / biber (CLAUDE.md → Model vs Code). Report the inconsistencies and the rule; mechanical reformat belongs in tooling, not hand-retyping that injects errors.

Phase 7: Cross-Reference Integrity (\ref ↔ \label)

1. Dangling refs — \ref \eqref \autoref \cref \Cref \pageref \nameref keys with no matching \label → ERROR.
2. Orphan labels — \label never referenced → WARNING (often harmless, but flag stale ones).
3. Display-item coverage — every figure/table is referenced in the text and vice versa (cross-check MANUSCRIPT_MAP.md → Figures & tables). An unreferenced figure or a "see Fig 3" with no Fig 3 is a defect.

Output Format

# Citation Audit — references.bib (+ 1 other .bib), 6 .tex files

> Live check: citation-gate.sh (runs on every .tex/.bib edit). This is the deep manual sweep.
> Reference style in force: ACL (numbered, ISO-4 abbreviations, sentence-case titles).

## ERRORS (block submission)
| Category | Item | Fix |
|---|---|---|
| Dangling \cite | `smith2022` cited in results.tex:88, not in any .bib | Supply verified entry OR flag [CITE] and remove key — do not invent |
| Duplicate key | `halluc2022` defined twice in references.bib | Merge; keep the complete entry |
| Placeholder DOI | `kumar2020`: doi = {10.xxxx/abcd} | Replace with real DOI from source, or drop the field |
| Empty field | `lee2018`: author = {} | Fill author from source or remove entry |
| Dangling \ref | `\ref{fig:horizon}` in discussion.tex:40, no \label | Add \label or fix the reference |

## WARNINGS (fix before submission)
| Category | Item | Fix |
|---|---|---|
| Orphan entry | `garcia2015` defined, never cited | Remove unless intentionally retained |
| Same work, 2 keys | `wang2021a` / `wang2021b` share DOI 10.18653/... | Merge to one key; update \cite sites |
| Author format | 3 entries use "First Last", rest "Last, First" | Normalize via biber, not by hand |
| Journal abbrev | `nguyen2020` uses full journal name; ACL wants ISO-4 | Abbreviate per ACL |
| Unreferenced figure | fig:appendixB has \label, never \ref'd | Reference it in text or move to appendix |

## Counts
- Cite keys: 47 cited / 52 defined → 5 orphans, 1 dangling
- DOIs: 41 present / 1 placeholder / 6 missing
- Cross-refs: 19 \ref / 19 \label → 1 dangling, 2 orphan labels

## Recommended fix order
1. Resolve the dangling \cite and \ref (blocks compile + the stop-gate).
2. Merge duplicate/same-work keys.
3. Replace placeholder DOI; fill empty required fields from sources.
4. Run biber/CSL to normalize author + journal formatting (deterministic — don't hand-edit).

Pairs With

• citation-gate.sh — the live, every-edit check (Phases 2 + 7). This skill goes deeper (Phases 3–6) and explains fixes. Read its verdict at .hook-state/last_quality_gate.json.
• stop-gate.sh — blocks turn completion while the last gate failed. A clean audit clears it. Bypass only with SKIP_QUALITY_GATE=1 for a pre-existing, unrelated dangling key.
• block-fabrication.sh — blocks writing placeholder DOIs / empty .bib fields. If a "fix" trips it, the fix was a fabrication.
• /claim-check — structural integrity here ≠ a cite licensing its claim. Run claim-check for the source-reading layer.

Notes

• Counting and key-resolution are deterministic — prefer a quick python3 parse over reasoning about which keys match. Reserve judgment for "are these two entries the same work?" and "is this orphan intentional?"
• Never assert a DOI is valid because it is well-shaped — shape ≠ existence. Verification against the real source is a separate, manual step.
• When converting reference styles, route the mechanical work through biber/a CSL processor; this skill audits, it does not retype the bibliography.