Validate Bibliography

Cross-reference citations in lecture files against bibliography entries. Two modes:

• Default (structural): missing entries, unused entries, malformed fields, typo candidates.
• --semantic: adds citation-drift detection (duplicate entries for the same paper), DOI verification via crossref, and citation-style consistency within each file.

Report saved to quality_reports/bib_audit_[structural|semantic].md.

Mode 1: Structural (default)

Steps

1. Read the bibliography file and extract all citation keys.

2. Scan lecture files for citation keys:

   • .tex: \cite{, \citet{, \citep{, \citeauthor{, \citeyear{, \textcite{, \parencite{
   • .qmd / .md: @key, [@key], [@key1; @key2]
   • Extract all unique citation keys used.

3. Cross-reference:

   • Missing entries (CRITICAL): cited in lectures, absent from .bib.
   • Unused entries (informational): in .bib but never cited.
   • Typo candidates: keys within edit-distance 2 of a .bib key (e.g., Smith2020 vs Smth2020).

4. Check entry quality:

   • Required fields present (author, title, year, journal/booktitle).
   • Author field properly formatted.
   • Year in 1900, current.
   • No malformed characters / encoding issues.
   • doi field normalized (no leading https://doi.org/).

5. Write report to quality_reports/bib_audit_structural.md.

Files scanned

Slides/*.tex
Quarto/*.qmd
guide/*.qmd
master_supporting_docs/**/*.tex

Bibliography location

Bibliography_base.bib at repo root by default; override via CLAUDE.md.

Mode 2: Semantic (--semantic)

Everything in Mode 1, plus:

2a. Citation drift detection

Multiple .bib entries describing the same paper under different keys. Symptoms:

• Smith2020 + Smith2020a with identical DOI or title.
• CallawaySantAnna2021 + CS2021 both pointing to the same paper.
• Collaborator-merged .bib files.