| name | check |
| description | Run a full project integrity check. Verifies pipeline files exist, params match, manuscript references resolve, and finds orphan files. Use periodically to catch inconsistencies. |
| allowed-tools | ["Read","Grep","Glob","Bash"] |
Pipeline Integrity Check
Run a full project integrity check in two phases.
Phase 1: Pipeline Integrity
- Script existence: Every script listed in
pipeline.md exists in code/
- Input data: Every input data file listed in pipeline exists
- Output directories:
output/logs/, output/figures/, output/tables/, output/results/ exist
- params.do values: Check that
code/stata/params.do has uncommented values for key parameters
- File location: No scripts or data files sitting in wrong directories
- 00_run.do consistency: Scripts in
00_run.do match those in pipeline.md
- run_all.sh consistency: Scripts in
run_all.sh match those in pipeline.md
Phase 2: Manuscript Audit
- Table/figure map: Every entry in pipeline.md Manuscript Figure Manifest has an existing output file and source script
- LaTeX references: Every
\input{} and \includegraphics{} in manuscript/main.tex resolves to an existing file
- Orphan outputs: Find any output files NOT referenced in the manuscript
- Undocumented references: Find any manuscript references NOT in the figure manifest
- Bibliography: Every
\cite key in manuscript has an entry in references.bib
Report
# Integrity Check: [Date]
## Pipeline
- Scripts found: N/M
- Missing scripts: [list]
- Missing data files: [list]
- Parameter issues: [list]
## Manuscript
- References resolved: N/M
- Missing files: [list]
- Orphan outputs: [list]
- Missing bib entries: [list]
## Status: [PASS / WARNINGS / FAIL]
Report all findings. Do not fix anything without user approval.
