musserlab/cleanup-scripts

Script Cleanup (Session Scope)

Check and consolidate working scripts from the current session. This skill focuses on the current session's work — for project-wide script health, use /audit-project.

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When to Run

• Before /done at the end of a coding session
• When scripts/scratch/ has accumulated working files
• When the user asks to clean up or consolidate scripts
• After a long iterative development session with lots of file creation

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Steps

1. Check scripts/scratch/

List all files in scripts/scratch/. For each file:

• Identify the target script: Based on the filename and conversation context, determine which numbered .qmd script this code belongs to. If no matching script exists, it may need a new numbered .qmd.
• Report to user: Show each scratch file, its proposed destination, and ask for confirmation before consolidating.
• Consolidate: Wrap the code in a proper .qmd chunk (using the quarto-docs skill template) and add it to the target script. Or create a new numbered .qmd if needed.
• Clean up: Delete the scratch file after successful consolidation.

If scripts/scratch/ is empty or doesn't exist, report "No scratch files" and move on.

2. Check for Convention Violations

Scan scripts/ (not subdirectories) for files that violate conventions:

• Numbered non-.qmd files: Files matching [0-9]*_*.R, [0-9]*_*.py, [0-9]*_*.Rmd in scripts/. On local, these should be .qmd — unless they carry a # allow-py: <reason> override comment in the first 20 lines, in which case .py is sanctioned. On the cluster, .py is the default and is fine without the override. Helpers belong in R//python/; superseded scripts in scripts/old/.
• Skip these: scripts/old/, scripts/scratch/, scripts/exploratory/, unnumbered files (legacy).

For each violation:

• Ask the user: convert to .qmd, move to helper dir (R/ or python/), or archive to scripts/old/?
• Execute the chosen action.

3. Verify Script-Output Correspondence

For each numbered .qmd in scripts/:

• Extract the number prefix (e.g., 15 from 15a_threshold.qmd).
• Check that outs/{number}_{topic}/ exists (using the lettered script convention — all scripts with the same number share one output dir).
• Flag scripts with no output directory (may indicate the script hasn't been run yet, which is fine for status: development).

For each output directory in outs/:

• Check that a corresponding numbered script exists in scripts/.
• Flag orphaned output directories (output dir exists but no script — may be from a deleted/archived script).

4. Report

Summarize:

• Scratch files consolidated (count)
• Convention violations found and fixed (count)
• Script-output mismatches (list)

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Important Notes

• This is session-scoped. It uses conversation context to understand what files belong where. For project-wide structural audits, use /audit-project.
• Never delete without asking. Always show what will be moved/deleted and get user confirmation.
• Respect legacy scripts. Unnumbered .Rmd files in scripts/ are legacy — do not flag them as violations.
• The hook should prevent most violations on local. The enforce-qmd-scripts.sh hook blocks creation of numbered non-.qmd files unless the file content carries a # allow-py: <reason> override comment in its first 20 lines. The hook auto-skips on the cluster (detected by /nfs/roberts/), where .py is the default. This skill catches anything that slipped through, pre-dates the hook, or used the override.