Use bib-check to audit citations in index.qmd against references.bib and report missing cited keys with manuscript line numbers, orphaned entries, duplicate bibliography keys with line numbers, and a totals summary.
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SKILL.md
name: bib-checkdescription: 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
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
Read references.bib and extract every entry key (the identifier after @article{, @book{, etc.)
Check for duplicate keys within references.bib (same key defined more than once)
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
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.