Pipeline Manifest

Build and maintain a pipeline.md that maps every script in a research project to its inputs, outputs, and the paper figures/tables it feeds. Optionally add structured headers to scripts that lack them.

When to Use

• When starting a multi-step empirical project (establish the pipeline early)
• Before sharing code with coauthors (makes the data flow legible)
• Before submission (ensures the replication package is traceable)
• After inheriting or reviving old code (pair with code-archaeology)
• When you can't remember which script produces Figure 3

When NOT to Use

• Pure theory projects with no empirical pipeline
• Single-script projects (no pipeline to map)
• Code quality review — use the code-review agent instead (this skill maps structure, not quality)

Modes