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 ```python # =======================...