researchby brycewang-stanford
Audit Citations and References
brycewang-stanford/bib-check
Cross-checks citation keys in index.qmd against references.bib, reporting missing, orphaned, and duplicate entries.
What it changes
Passed 15 of 21 test cases with the skill, and 11 of 21 without it.
Without skill50%
With skill73%
Checks it passed that the model alone missed
- Groups missing cited keys under Errors
- Groups uncited bib keys under Orphaned
- Groups repeated bib keys under Duplicates
and 4 more in the full report
5 fixed11 passed either way6 still failing0 broke
- Pass-rate lift
- +23 pp
- Tokens
- +4%
- Agent turns
- 0%
- Response time
- -18%
Model gemini-3.6-flashMeasured 8/9/2026v116 of 22 cases passed with skill · 21 comparable
See it in action
One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.
PromptThe entry `taylor2015` exists in `references.bib` at line 30, but `@taylor2015` never appears in `index.qmd`. How is `taylor2015` categorized?
What was checked, without and with the skill| Checked | Without skill | With skill |
|---|
| Classifies taylor2015 under the Orphaned category | Missed | Passed |
|---|
What's inside
The instructions your model reads when the skill loads.
SKILL.md33 linessingle file
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.
Track record
Benchmark
15 / 21
test cases passed, vs 11 / 21 without
Adoption
- Users
- 0
- Times used
- 0
Safety and source details
SkillSafety
✓ 3 of 3 passed✓Code scan15 of 15 checks clean
0 critical · 0 warning · 0 info — scanner v4 — 8/2/2026
View 15 scanner checks
live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing
✓IntentSafe
LLM judge · does the skill do what it claims
✓ContentClean
LLM judge · policy & harmful-content review
Source
Importedbrycewang-stanford / Auto-Empirical-Research-Skills
skills/29-quarcs-lab-project20XXy/dot-claude/skills/bib-check/SKILL.md
License NOASSERTIONImported 8/2/2026Version v1