Bib Filter

Bibliography Filter

Produce a filtered.bib containing only the .bib entries actually cited in the LaTeX project.

When to Use

• Before submission — strip unused references from the bibliography
• When a shared .bib (e.g., Paperpile/Paperpile export) contains hundreds of entries but the paper cites a subset
• To reduce .bib file size for Overleaf or arXiv upload
• As a cleanup step after major revision (removed sections may leave orphan citations)

Process

Step 1: Locate files

If given a directory, find the main .tex and .bib files:

• .tex: Glob for *.tex in the directory (and paper/ subdirectory if it exists). The main file is the one containing \begin{document}.
• .bib: Look for \bibliography{...} or \addbibresource{...} in the main .tex to find the bib filename. Fall back to globbing *.bib.

If given a specific .tex file, derive the .bib from it.

Step 2: Extract all citation keys from .tex

Scan all .tex files in the project (main + any \input{}/\include{} files) for citation commands:

\cite{key1,key2}
\citep{key1,key2}
\citet{key1}
\citealt{key1}
\citealp{key1}
\citeauthor{key1}
\citeyear{key1}
\citetext{key1}
\parencite{key1,key2}
\textcite{key1}
\autocite{key1}
\footcite{key1}
\fullcite{key1}
\nocite{key1}

Handle:

• Multiple keys in one command: \cite{key1,key2,key3} → extract all three
• Whitespace around commas: \cite{key1, key2} → trim
• Optional arguments: \cite[p.~5]{key1} or \citep[see][]{key1} → extract key1
• \nocite{*} → special case: means "include everything", so filtered.bib = full .bib (warn and stop)

Collect into a deduplicated set of cited keys.

Step 3: Parse .bib and filter

Read the .bib file. For each entry (@article{key,, @book{key,, @inproceedings{key,, etc.):

• If the entry's key is in the cited set → include in output
• If not → exclude
• Preserve @string{}, @preamble{}, and @comment{} blocks (they may be needed by included entries)

Step 4: Write filtered.bib

Write filtered.bib in the same directory as the original .bib.

Report:

Original: N entries
Cited: M keys found in .tex
Filtered: M entries written to filtered.bib
Removed: N-M unused entries

If any cited keys are not found in the .bib, list them as warnings (these are missing references — suggest running /bib-validate).

Step 5: Suggest next steps

• "Replace references.bib with filtered.bib?" — ask before overwriting
• If missing keys were found: "Run /bib-validate to resolve M missing citation keys"

Edge Cases

• Multiple .bib files: If the project uses multiple bib files (\bibliography{refs1,refs2}), read all of them and produce a single filtered.bib combining only cited entries
• \nocite{*}: Warn that all entries are cited and stop — filtering would be a no-op
• Cross-references: Some .bib entries use crossref = {parent-key}. If a cited entry cross-references another, include the parent even if it's not directly cited
• Empty result: If no citations found in .tex, warn and do not write an empty file

Output Verification (Guard)

This skill writes files. Before any auto-commit, emit an outputs manifest and run the shared verifier. See skills/_shared/verify-outputs.md for the full protocol.

Required tail steps (before git commit):

1. Write manifest to <project>/.Codex/state/outputs-manifest-<UTC-timestamp>.json listing every file this skill claims to have written in this invocation (paths relative to the project root).

2. Run:

   python3 "$HOME/.Codex/skills/_shared/verify_outputs.py" \
       --manifest "$MANIFEST" \
       --project-root "$PROJECT_ROOT"
   

3. If the verifier exits non-zero, do not commit — surface the missing-files list to the user and stop. The verifier has already logged an error entry to ~/.Codex/ecc/skill-outcomes.jsonl, which feeds the launcher dashboard.

Why: closes the "hallucinated outputs" failure class (commit b2cff75, 2026-04-18).