check-refs - SKILL.md Agent Skill

name: check-refs user_invocable: true description: Verify citation references in a LaTeX paper. Checks that all cited papers exist in academic databases, flags suspicious entries, and suggests missing DOIs/URLs. Use when the user wants to check references, verify citations, or before submission.

check-refs — Citation Reference Check

Verify all references in a LaTeX paper against academic databases.

When to Use

"check my references", "verify citations", "check refs"
Called by the presubmit-checks skill as one of its checks
Before submitting a paper draft

Workflow

1. Find the paper files

Look for .tex and .bib files. Common project structures:

paper/current/main.tex + paper/current/main.bib (standard project template)
paper/current/main.tex + paper/current/references.bib
paper/main.tex + paper/main.bib (flat layout)
main.tex + references.bib (root-level)

Search order:

If user provides a path, use it
Look for paper/current/main.tex
Look for paper/main.tex
Look for main.tex in current directory
Glob for **/*.tex and pick the main file (the one with \begin{document})

For .bib: look for main.bib or references.bib next to the .tex file, or let bibsleuth auto-detect from \bibliography{}.

2. Run existence check (fast, no API key needed)

Run in the background with a 10-minute timeout — bibsleuth queries multiple academic APIs and can take several minutes for large bibliographies. Bibsleuth writes bibsleuth-report.json and bibsleuth-report.md next to the input file by default.

# Use Bash tool with run_in_background: true, timeout: 600000
uvx bibsleuth check <TEX_FILE> --bib <BIB_FILE> --no-llm

Tell the user the check is running in the background and continue with other work. You will be notified when it completes.

3. Present results

Once notified that the command finished, read the bibsleuth-report.md file (in the same directory as the input file) and summarize:

The report is grouped by verdict (verified, likely, unverified, error) and entry category (academic papers, books, software/data)
Focus on unverified entries — these need attention
List suggested patches (missing DOIs, URLs) from the patches section
Tell the user where the full report file is

4. Offer next steps

Apply patches: offer to add suggested DOIs/URLs to the .bib file (ask before editing)
Full LLM analysis: if user wants mis-citation detection and missing citation suggestions, run without --no-llm (requires ANTHROPIC_API_KEY or OPENAI_API_KEY). Also run in background with 10-minute timeout:
```
uvx bibsleuth check <TEX_FILE> --bib <BIB_FILE>
```
Save to library: uvx bibsleuth library add <BIB_FILE>

5. LLM analysis results (if run)

Summarize additional findings:

Mis-citations: cited paper may not support the claim made in the text
Suggested papers: candidates for claims that could use stronger citations
Contradictions: well-cited papers that argue against claims in the paper

Rules

Always run --no-llm first — it's fast and free
Don't automatically edit the .bib — ask before applying patches
If bibsleuth is not installed, run uv tool install bibsleuth first