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

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

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

1. 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

1. 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.