Audit References

Audit references (citation verification)

This skill verifies that the citations in a document actually say what the author claims they say. It complements update-references (which discovers new papers) by auditing existing citations for correctness.

The output is an audit report: one entry per citation, with a verdict (supported, unsupported, misattributed, not-found) and the evidence from the source paper.

Where things live

• Document: The markdown file the user points you at, or the most obvious draft in the working directory. Look for .md files that contain [@ citations.
• Database: references.yaml in the working directory (or at the nearest ancestor that has one). This is the Citation Style Language (CSL) YAML bibliography that pandoc and update-references both use.
• PDFs/papers: <db-dir>/pdfs/ and <db-dir>/papers/ — the same locations update-references uses. If a paper was already fetched, reuse its markdown.
• Audit report: <db-dir>/audits/<document-stem>-audit.md, using the template in <skill>/references/audit-template.md.

Prerequisites

The document must use pandoc citation syntax: [@citation-id], [@id1; @id2], or @citation-id inline. The citation ids must match entries in references.yaml.

If references.yaml does not exist in the paper directory, stop and tell the user. They need to create it first (using update-references or manually).

Running the scripts

This skill and the update-references scripts it calls run in the pixi-managed environment that ships beside the skills. The agent provisions it on repo open via <agent-dir>/scripts/ensure-env.sh; the commands below use $RUN:

RUN="pixi run --manifest-path <skill>/../../pixi.toml python"

No pip install is needed — the environment supplies PyYAML and the PDF libraries.

The workflow

1. Extract citations

Run the extraction script to get every citation and its surrounding context:

$RUN <skill>/scripts/extract_citations.py <document-path>

This outputs a JSON array of objects, each with:

• citation_id: the pandoc citation key
• context: the sentence or paragraph surrounding the citation
• line: the line number in the source document
• claim: a best-effort extraction of the claim being made (the sentence containing the citation)

Review the output. If the document has no citations, report that and stop.

2. Resolve against references.yaml

Load references.yaml and match each citation_id to an entry. Classify each citation:

• resolved: the id matches an entry in references.yaml
• unresolved: no matching entry — flag this immediately in the report

For resolved citations, note the entry's arxiv_id (if present), URL, title, and author fields. These are needed to fetch the paper.

3. Fetch and read cited papers

For each resolved citation, get the paper text:

1. Already fetched? Check if md_path (or legacy text_path) or pdf_path exists in the database entry and the file is on disk. If so, read the markdown file directly. If only a PDF exists without markdown, run repair first to generate it.

2. Has arxiv_id? Fetch via the sibling skill's script:

   $RUN .agents/skills/update-references/scripts/arxiv.py \
     --db <db-path> fetch --id <arxiv_id>
   

   Then read the markdown conversion it produces.

3. No arxiv_id? Search Google Scholar for the title:

   $RUN .agents/skills/update-references/scripts/scholar.py \
     --db <db-path> search --query "<paper title>" --max 3
   

   If a match is found with a PDF link, fetch it:

   $RUN .agents/skills/update-references/scripts/scholar.py \
     --db <db-path> fetch --title "<title>" --url "<pdf_url>" \
     --authors "Given Family" --year YYYY
   

4. Cannot fetch? Mark the citation as not-found in the report and move on.

4. Verify claims

For each citation where you have the paper text, read the relevant sections and evaluate the claim made in the citing document:

• supported: the source paper contains evidence that backs the claim. Quote the relevant passage (one or two sentences).
• unsupported: the source paper does not contain evidence for the claim. Explain what the paper actually says about the topic.
• misattributed: the claim is true but attributed to the wrong source, or the source says something different from what is claimed. Explain the discrepancy.
• not-found: the paper could not be located or accessed.

Be precise. A claim like "Smith et al. show 30% improvement" requires finding that specific number in the source. A paraphrase like "Smith et al. demonstrate significant gains" needs the source to actually demonstrate gains in the claimed domain.

5. Write the audit report

Use the template at <skill>/references/audit-template.md. Write the report to <db-dir>/audits/<document-stem>-audit.md.

6. Report back

Summarize the results:

• Total citations found
• How many resolved vs. unresolved
• Verdicts: N supported, N unsupported, N misattributed, N not-found
• Call out any unsupported or misattributed citations explicitly — these need the author's attention

Dependencies

Same as update-references: the shared pixi environment supplies PyYAML and pymupdf4llm for PDF-to-markdown conversion, provisioned by ensure-env.sh with no pip install. The extraction script is pure Python stdlib. arXiv and Scholar access use the sibling skill's scripts, run through the same $RUN wrapper.