Our review
Runs a full project integrity check: pipeline coherence (scripts, data, parameters) and manuscript audit (figures, tables, references).
Strengths
- Catches missing or misplaced scripts, data, or outputs.
- Verifies consistency between README, scripts, and manuscript.
- Identifies orphan files and undocumented references.
- Never modifies anything without explicit user approval.
Limitations
- Relies on the accuracy and currency of the README.
- Does not fix issues automatically.
- Only checks items explicitly listed in README and manuscript.
Use this skill before submission or sharing to ensure project reproducibility and consistency.
Avoid it when the project lacks a structured README or a LaTeX manuscript to audit.
Security analysis
SafeThe skill instructs the agent to perform read-only integrity checks on project files, directories, and references. It does not involve executing scripts, modifying files, accessing network resources, or handling sensitive data. No destructive or exfiltrating actions are present.
No concerns found
Examples
Run a full project integrity check on this repository, covering both the pipeline and manuscript audit.Audit the pipeline: verify that all scripts in the README table exist, data files are present, and params match the README parameters table.Cross-check the manuscript.tex against the table/figure map: verify includegraphics and input files exist, and report orphaned outputs.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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