check

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

1. Script existence: Every script listed in pipeline.md exists in code/
2. Input data: Every input data file listed in pipeline exists
3. Output directories: output/logs/, output/figures/, output/tables/, output/results/ exist
4. params.do values: Check that code/stata/params.do has uncommented values for key parameters
5. File location: No scripts or data files sitting in wrong directories
6. 00_run.do consistency: Scripts in 00_run.do match those in pipeline.md
7. run_all.sh consistency: Scripts in run_all.sh match those in pipeline.md

Phase 2: Manuscript Audit

1. Table/figure map: Every entry in pipeline.md Manuscript Figure Manifest has an existing output file and source script
2. LaTeX references: Every \input{} and \includegraphics{} in manuscript/main.tex resolves to an existing file
3. Orphan outputs: Find any output files NOT referenced in the manuscript
4. Undocumented references: Find any manuscript references NOT in the figure manifest
5. 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.