Our review
Runs a full integrity audit of a research project, checking both pipeline consistency (scripts, data, parameters) and manuscript completeness (figures, references).
Strengths
- Detects missing or misplaced files in the pipeline.
- Verifies parameter values match between README and code.
- Identifies unreferenced output files or manuscript references.
- Read-only; never modifies anything without user approval.
Limitations
- Relies on a specific project structure (README tables, LaTeX commands).
- Does not validate scientific content or result correctness.
- May produce false positives for non-standard project organizations.
Before submitting a paper or sharing a project, to ensure all components are in place and consistent.
For projects without a defined pipeline or LaTeX manuscript, where integrity checks are less meaningful.
Security analysis
SafeThe skill instructs only read-only checks (file existence, directory structure, string matching) and explicitly forbids fixing anything without approval. It does not contain any destructive, exfiltrating, or obfuscated commands.
No concerns found
Examples
Run a full project integrity check on the current project. Report all findings without making any changes.Audit the manuscript.tex file for missing figure files and check the figure/table map in the README is complete. Don't fix anything.Check that all scripts listed in the README pipeline table exist, that input data files are present, and that output directories are created. Report any discrepancies.Run a full project integrity check. Two phases:
Phase 1 — Pipeline integrity: (1) Every script listed in README pipeline table exists. (2) Every input data file listed exists. (3) No scripts or data files sitting in wrong directories. (4) Output directories exist. (5) params.do values match README parameters table.
Phase 2 — Manuscript audit: (1) Every entry in README table/figure map has an existing output file and source script. (2) Every \includegraphics and \input in manuscript.tex resolves to an existing file. (3) Find any output files not referenced in the manuscript (orphans). (4) Find any manuscript references not in the table/figure map (undocumented).
Report all findings. Do not fix anything without user approval.
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