verify-references

name	verify-references
description	Verify and validate bibliography references in BibTeX files by comparing with CrossRef metadata. Use when user asks to check, verify, or validate references.

When this skill is invoked, you must:

Step 0: Pre-check

1. Ask user for:

   • bib_file path (e.g., Biblio/ref.bib)
   • tex_dir path (e.g., Tex/)

2. Generate report file path: <bib_file_dir>/verification_report.md

3. Check if report already exists:

   • If exists: Use AskUserQuestion tool to ask "Found existing verification report at <report_path>. What would you like to do?" with options:
     • "Re-run verification" (description: "Delete existing report and run full verification again")
     • "View existing report" (description: "Read and summarize the existing report without re-running")
   • If user chooses "View existing report": Read and summarize the existing report, then exit
   • If user chooses "Re-run verification" or report doesn't exist: Continue to Step 1

Step 1: Check Unused References

1. Run: python ${CLAUDE_SKILL_DIR}/check_unused_refs.py <bib_file> <tex_dir>

2. Parse JSON output and write to report file:

   • Create report with header "# Bibliography Verification Report"
   • Add section "## Unused References"
   • List total references, cited count, uncited count
   • List uncited citation keys

Step 2: Download CrossRef Metadata

1. Generate output file path: <bib_file_dir>/ref_crossref.bib

2. Tell user: "Downloading CrossRef metadata. You can monitor progress in real-time by viewing <full_path_to_ref_crossref.bib>"

3. Run: python -u ${CLAUDE_SKILL_DIR}/download_crossref.py <bib_file> <output_file>

   • Queries CrossRef API for all entries with DOIs
   • Generates a CrossRef version of the bib file for comparison
   • Maintains the same entry order as the original file
   • Monitor and relay progress: As the script outputs progress lines like "[1/50] Querying key: DOI", relay these to the user in real-time so they can see the download progress

4. Report progress summary:

   • Total entries processed
   • Entries with DOIs
   • Entries without DOIs (skipped)

Step 3: Generate Comparison Report

1. Run: python ${CLAUDE_SKILL_DIR}/compare_refs.py <bib_file> <crossref_bib> <report_file>

   • Use the same <bib_file_dir>/verification_report.md from Step 1
   • Compares original bib file with CrossRef version
   • Identifies discrepancies in metadata fields
   • Calculates similarity scores
   • Appends comparison results to the existing report

2. Parse and present the comparison section:

   • Summary statistics
   • Entries with no discrepancies
   • Entries with discrepancies (sorted by similarity)
   • Detailed field-by-field comparison table

Step 4: Final Summary

1. Read the complete verification report from <bib_file_dir>/verification_report.md

2. Provide a concise summary to the user:

   • Number of unused references
   • Number of entries verified against CrossRef
   • Number of entries with discrepancies
   • Key issues found (if any)

3. Tell the user: "Detailed report saved to: <full_path_to_verification_report.md>"