name: bib-check description: Cross-checks citation keys in index.qmd against references.bib, reporting missing, orphaned, and duplicate entries. Use when verifying citations. allowed-tools: Bash, Read, Glob, Grep

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.