pipeline-manifest

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

Ask the user which mode to run:

Mode	What it does	Writes to
Scan (default)	Read-only. Scans scripts, builds pipeline.md	pipeline.md only
Add headers	Scan + insert structured headers into scripts that lack them	pipeline.md + script files

In Add headers mode, show the proposed header for each script and get confirmation before writing. Never overwrite an existing structured header — only add to scripts that lack one.

Structured Script Header Format

Every research script should begin with a structured header block. The format adapts to the language:

Python

# ============================================================================
# PURPOSE: [One sentence describing what this script does]
# INPUTS:  [Comma-separated list of input files, relative to project root]
# OUTPUTS: [Comma-separated list of output files, relative to project root]
# DEPENDS: [Scripts that must run before this one, or "none"]
# PAPER:   [Figure/table references this feeds, e.g. "Figure 2, Table 1", or "none"]
# ============================================================================

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