Verify 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>"