galaxyproject / galaxyproject/foundry

Galaxy pipeline Molds write fixed filenames to cwd — namespace per-source run

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bug priority/v2 roadmap/off
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TypeScript
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Description

> Posted by Claude (AI assistant) on behalf of @jmchilton — not authored by them personally.

## Summary

The `*-summary-to-galaxy-*` pipeline Molds each write a **fixed filename to the current working directory**. Running the pipeline inside a repo drops a pile of untracked artifacts in the root, and a second run collides with the first.

## Observed

One INTERVIEW → GALAXY run produced, all in cwd (the foundry worktree root):

- `freeform-summary.md`
- `freeform-galaxy-interface.md`
- `freeform-galaxy-data-flow.md`
- `iwc-comparison-notes.md`
- `galaxy-workflow-draft.gxwf.yml`

Issues:

- clutter — 5 untracked files in the repo root,
- collision — two runs of the same pipeline overwrite each other,
- no grouping — artifacts from one source aren't namespaced together.

## Suggestion

- write into a per-source working subdir (slug derived from the source id / title), or
- accept an output-dir argument threaded through the pipeline.

Preserve the current filenames *within* that dir so downstream Molds' input wiring stays stable.

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