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Bib Check

Documents
bib-check

Bib Check is an Agent Skill for documents published in the brycewang-stanford/Auto-Empirical-Research-Skills repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

Cross-checks citation keys in index.qmd against references.bib, reporting missing, orphaned, and duplicate entries. Use when verifying citations.

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How to use this skill

Bring this guide into your coding agent with a prompt tailored to the tool you use.

  1. Open your project in Codex.
  2. Copy and paste the prompt below.
  3. Review files and risks before approving any action.
Prompt to paste
Inspect the Agent Skill at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/blob/HEAD/skills/29-quarcs-lab-project20XXy/dot-claude/skills/bib-check/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/bib-check, but wait for my approval before writing files or running scripts.

Copying this prompt does not install or run the skill. Review third-party files before use.

Audit Citations and References

Cross-check all citation keys in the manuscript against references.bib and report mismatches.

Steps

  1. Read index.qmd and extract every citation key:

    • Narrative citations: @key
    • Parenthetical citations: [@key], [@key1; @key2]
    • Ignore email addresses and @sec-, @fig-, @tbl- cross-references

  2. Read references.bib and extract every entry key (the identifier after @article{, @book{, etc.)

  3. Check for duplicate keys within references.bib (same key defined more than once)

  4. Report three categories:

    Errors — cited in manuscript but missing from .bib:

    • List each missing key with the line number in index.qmd where it appears
    • For each, suggest running /project:cite <key> to add the entry

    Orphaned — in .bib but never cited in manuscript:

    • List each unused key (informational, not necessarily a problem)

    Duplicates — same key appears multiple times in .bib:

    • List each duplicate with line numbers in references.bib

  5. Print a summary: total cited keys, total .bib entries, errors, orphaned, duplicates

Error handling

  • If references.bib does not exist, report the error and stop.
  • If index.qmd contains no citations, report "No citations found" and stop.