version: "1.0.3" name: bib-validate description: "Cross-reference \\cite{} keys against .bib files or embedded \\bibitem entries. Finds missing, unused, and typo'd citation keys. Deep verification mode spawns parallel agents for DOI/metadata validation at scale. Fix mode auto-adds missing entries to Paperpile." allowed-tools: Read, Glob, Grep, Task, Write, Bash(mkdir), Bash(ls), Bash(rm), Bash(paperpile) argument-hint: "[project-path or tex-file] [--verify-doi] [--fix]"

Bibliography Validation

LIBRARY-FIRST RULE: ALWAYS cross-reference cited keys against Paperpile (`paperpile search-library`) during validation. This catches drift between the .bib file and the reference manager. See the Reference Manager Cross-Reference section.

Output Path

Per rules/review-artefact-routing.md (auto-loads in research projects (path-scoped to paper-*/ and paper/)):

• Source slug: bib-validate
• Write reports to: reviews/bib-validate/YYYY-MM-DD.md inside the project. Path is relative to the research project root, not the Task-Management repo.
• Never at project root (./CRITIC-REPORT.md-style filenames are forbidden — pre-rule layout).
• Idempotency: if today's file exists, append a same-day descriptor ({date}-revision.md, {date}-r2.md, {date}-pre-submission.md) — never overwrite.
• Index update: if reviews/INDEX.md exists, write a one-line entry under "Latest per source" pointing at the new file. Otherwise /review-recap will rebuild the index next time it runs.
• Infrastructure repos (Task-Management, atlas-workspace, etc.): this section does not apply — the path-scoped rule won't load there.

Modes

When to Use

• Before compiling a final version of a paper
• After adding new citations to check nothing was missed
• When biber/bibtex reports undefined citations
• As part of a pre-submission checklist (pair with /proofread)

When NOT to Use

• Finding new references — use /literature for discovery
• Building a bibliography from scratch — use /literature with .bib generation
• General proofreading — use /proofread (which also flags citation format issues)

Phase 0: Session Log (Suggested)

Bibliography validation with preprint staleness checks can be context-heavy (OpenAlex lookups, web searches for published versions). Before starting, suggest running /session-log to capture prior work as a recovery checkpoint. If the user declines, proceed without it.

Convention

Default bibliography file is `references.bib` — this is the standard across all projects (per the /latex skill convention). However, the skill also supports:

• Any .bib file found in the same directory as the .tex files being audited
• Embedded bibliographies using \begin{thebibliography} / \bibitem{key} blocks
• Both external and embedded simultaneously (rare but possible)

Bibliography Detection

At the start of validation, detect which bibliography method the project uses:

1. External .bib file (standard)

Look for .bib files in the project directory. Priority order:

1. references.bib (preferred — standard naming convention across all projects)
2. Any other .bib file in the same directory as the .tex files

If multiple `.bib` files are found, validate all of them and produce a combined report. Note which file each issue belongs to. If a legacy-named .bib file (e.g., paperpile.bib) exists alongside references.bib, flag it as a potential cleanup opportunity (the project may have migrated from Paperpile).

Full validation applies: cross-reference checks and quality checks.

2. Embedded \begin{thebibliography} / \bibitem{key}

Some LaTeX documents define references inline rather than using an external .bib file. Detect by scanning .tex files for \begin{thebibliography}.

Extract keys from \bibitem entries:

• \bibitem{key} — standard form, key is the argument in braces
• \bibitem[label]{key} — optional label form (e.g., \bibitem[Smith et al., 2020]{smith2020}), key is in the second set of braces

Only cross-reference checks apply (missing keys, unused keys, typos). Quality checks (required fields, year, author formatting) are skipped because embedded bibliographies don't have structured metadata.

3. Both (rare)

If a project has both a .bib file and \begin{thebibliography} blocks, validate both:

• Run full validation on the .bib file
• Run cross-reference checks on \bibitem entries
• Merge both key sets when checking for missing citations

Workflow

1. Find files: Locate all .tex files in the project
2. Detect bibliography type: Check for .bib files and/or \begin{thebibliography} blocks
3. Extract citation keys from .tex: Scan for all citation commands
4. Extract entry keys from bibliography source(s):

• External: Parse all @type{key, entries from .bib file(s)
• Embedded: Parse all \bibitem{key} and \bibitem[label]{key} entries

1. Cross-reference: Compare the two sets
2. Quality checks: Validate .bib entry completeness (external only)
3. Produce report: Write results to stdout (or save if requested)

Citation Commands to Scan

Scan .tex files for all of these patterns:

Also handle multi-key citations: \citep{key1, key2, key3}

Cross-Reference Checks

Critical: Self-citation deanonymization (double-blind submissions only)

When --double-blind is set OR when a paper-* directory's vault submission frontmatter shows the venue is double-blind, run a self-citation scan in addition to the standard checks.

1. Load submission author list. Read ~/Research-Vault/submissions/<paper-slug>-<venue>-<year>.md authors: / coauthors: field. If absent, prompt: Submission author surnames (comma-separated):. Refuse to proceed without a non-empty list.
2. For each `.bib` entry, parse the `author = {...}` field. Tokenize by and and extract surnames.
3. Compare against the submission author list. If the cited entry's author surnames are a subset of the submission's (or the cited entry has authors that exactly match), flag the citation.
4. Severity: Critical. Self-citation by name is a desk-reject trigger at every major double-blind security/ML venue (CCS, NDSS, S&P, USENIX, ICML, NeurIPS, ICLR). Third-person grammar in the body text alone does NOT cure the issue when the bib entry itself names the authors — see _shared/double-blind-anonymity-checklist.md §P4.
5. Output format:

`` ⚠ SELF-CITATION DEANONYMIZATION (Critical) references.bib:42 burnat2026paradox authors: the user A D Burnat and Brittany I [Collaborator] overlaps: Burnat (1/1), [Collaborator] (1/1) → ALL submission authors named remediation: author = {Anonymized for double-blind review}, title = {Title withheld; preprint anonymized}, note = {Anonymized self-citation} AND in the body text, replace any "Burnat and [Collaborator] [N]" with "Prior work by the authors [N]" or similar. ``

1. Also scan `.tex` body near each flagged \cite{<key>} for any of the cited entry's surnames within ±200 chars. Flag those occurrences with file:line so the user can de-name the prose alongside the bib fix.

This check is a desk-reject prevention gate (see incident log in _shared/double-blind-anonymity-checklist.md). Run it before the standard cross-reference checks so the user sees the most-severe finding first.

Critical: Missing Entries

Citation keys used in .tex but not defined in the bibliography source (.bib file or \bibitem entries).

These will cause compilation errors.

Warning: Unused Entries

Keys defined in the bibliography source but never cited in any .tex file.

Not errors, but may indicate:

• Forgotten citations (should they be \nocite?)
• Leftover entries from earlier drafts
• Entries intended for a different paper

Warning: Possible Typos (Fuzzy Match)

For each missing key, check if a similar key exists in the bibliography using edit distance:

• Edit distance = 1: Very likely a typo
• Edit distance = 2: Possibly a typo
• Flag these with the suggested correction

Common typo patterns:

• Year off by one: smith2020 vs smith2021
• Missing/extra letter: santanna vs sant'anna vs santana
• Underscore vs camelCase: smith_jones vs smithjones

Reference Manager Cross-Reference

After the disk-based cross-reference, check each cited key against Paperpile. Produces a status table (HEALTHY / DRIFT / EXPORT_GAP / MISSING).

Full steps, MCP calls, and status categories: `references/ref-manager-crossref.md`

Quality Checks on .bib Entries

These checks apply only to external `.bib` files. Embedded bibliographies lack structured metadata, so quality checks are skipped for them.

Required Fields by Entry Type

Year Reasonableness

• Flag entries with year < 1900 or year > current year + 1
• Flag entries with no year at all

Author Formatting

• Check for inconsistent author formats within the file
• Flag entries where author field contains "and others" or "et al." — this is never valid in BibTeX. All authors must be listed explicitly. Severity: Warning.
• Flag entries with organisation names that might need {{braces}} to prevent splitting

DOI Verification & Fabrication Detection

See `references/doi-verification.md` for hard rules, resolution protocol, and LLM-hallucination detection.

Preprint Staleness Check

For every entry that looks like a preprint, check whether a peer-reviewed version has since been published. Full detection signals, lookup protocol, and classification: `references/preprint-check.md`

Severity Levels

Bibliography Output

After validation, offer these actions if applicable:

• Embedded bibliography → offer to create `references.bib`: If the project uses \begin{thebibliography}, offer to extract the references into a proper references.bib file (one @misc entry per \bibitem, with the full text as a note field). The author can then enrich the entries with proper metadata.
• Non-standard `.bib` name → offer to rename: If the existing .bib file is not named references.bib, offer to rename it to references.bib and update the \bibliography{} command in the .tex file.

These are offers only — do not make changes without explicit confirmation.

Report Format

Full report template with all sections: `references/report-template.md`

Sections: Summary table → Critical (missing entries) → Warning (typos, unused, missing fields, DOI mismatches, stale preprints) → Info (year issues) → Limitations (for embedded bibliographies).

Optional: Metadata Verification

See `references/metadata-verification.md` for Paperpile and scholarly CLI lookup workflows.

Deep Verification Mode (Parallel, Disk-Based)

See `references/deep-verify-protocol.md` for auto-trigger thresholds (≥40 entries) and sub-agent architecture.

Council Mode (Optional)

For high-stakes submissions. Trigger: "council bib-validate", "thorough bib check". Full details: `references/council-mode.md`

Fix Mode

After producing the validation report, automatically fix resolvable issues in the project .bib (DRIFT → correct the BibTeX; MISSING → search + add to the .bib, then stage for Paperpile import via paperpile write-bib; MIGRATE → stage updated entry; metadata → correct BibTeX). Library additions are staged as a paperpile-stage-*.bib for manual import — the Paperpile CLI is read-only.

Full auto-fix actions, post-fix maintenance, and skip conditions: `references/fix-mode.md`

Quality Scoring

When producing a full validation report, apply numeric quality scoring using the shared framework:

• Framework: `../shared/quality-scoring.md` — severity tiers, thresholds, verdict rules

Map validation findings to the framework tiers:

• Critical (-15 to -25): Missing entry for a cited key (compilation error)
• Major (-5 to -14): DOI mismatch, likely fabricated reference (LLM-drafted hallucination), stale preprint with published version available, "et al." in author field
• Minor (-1 to -4): Missing optional fields, year oddities, unused entries

Compute the score and include the Score Block in the report after the summary table.

Log to REVIEW-STATE.md (final step)

Write the bib-validate report to reviews/bib-validate/<YYYY-MM-DD-HHMM>.md (mkdir -p reviews/bib-validate/ first). Then append a row to the project's REVIEW-STATE.md:

bash ~/.claude/skills/_shared/review-state-log.sh \
  --check bib-validate \
  --paper "<paper-{venue} dir>" \
  --verdict "<PASS|ISSUES FOUND>" \
  --score "<numeric score from quality-scoring framework, or —>" \
  --open-issues "<missing-plus-unused-plus-typo-count>/<missing-plus-unused-plus-typo-count>" \
  --report "reviews/bib-validate/<YYYY-MM-DD-HHMM>.md" \
  --notes "<one-line: e.g. '2 missing keys, 5 unused; 1 likely fabricated'>" \
  [--trigger "pre-submission-report|review-cluster"]

• Verdict: PASS if no missing/unused/typo'd citations; ISSUES FOUND otherwise.
• Score: the numeric quality score if computed; — otherwise.
• Open issues: total of (missing + unused + typo'd) at run time.
• Trigger: pass orchestrator name only if invoked via /pre-submission-report or /review-cluster. Otherwise omit.

Schema: ~/Task-Management/docs/reference/review-state-schema.md.

Cross-References

• `/proofread` — For overall paper quality including citation format
• `/literature` — For finding and adding new references (includes full OpenAlex workflows)
• `/bib-coverage` — Compare project .bib vs Paperpile label — find uncited papers and unfiled references
• `/latex` — For compilation with reference checking
• `/latex` — For compilation and error resolution. Run after fixing bibliography issues to verify citations compile cleanly.
• `shared/reference-resolution.md` — Canonical lookup + filing sequence used by Ref Manager Cross-Reference and Fix Mode