Project Integrity Check

VerifiedSafe

Run a full project integrity check including pipeline integrity and manuscript audit. Reports all findings without making changes.

Sby Skills Guide Bot
DevelopmentIntermediate
107/30/2026
Claude CodeCursorWindsurf
#project-integrity#reproducibility#pipeline-audit#manuscript-audit

Recommended for

Our review

Runs a full project integrity check in two phases: pipeline (scripts, data, parameters) and manuscript (figures, tables, references).

Strengths

  • Systematic detection of missing or misplaced files
  • Cross-validation between README and actual code
  • Audit of LaTeX manuscript dependencies

Limitations

  • Does not verify file content correctness
  • Relies on README and parameter table accuracy
  • May produce false positives if project structure deviates from conventions
When to use it

Best used before submission or deployment to ensure project consistency.

When not to use it

Avoid for projects without clear documentation or non-reproducible pipelines.

Security analysis

Safe
Quality score83/100

The skill performs only validation checks (file existence, directory integrity, reference consistency) and instructs only reporting; no destructive, network, or data exfiltration actions.

No concerns found

Examples

Full integrity check
Run a full project integrity check on this project: verify pipeline scripts exist, data files are present, output directories are created, parameters match README, and manuscript references are consistent.
Phase 1 – pipeline check only
Check the pipeline integrity of this project: confirm all scripts listed in the README pipeline table exist, input data files are in place, no stray files in wrong directories, output directories exist, and params.do values match the README parameters table.

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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