cleanup-notebooks

name	cleanup-notebooks
description	Clean up and reorganize markdown in enriched Jupyter notebooks. Arguments: [target] [--dry-run] [--aggressive] [--hierarchy-only]

Cleanup Notebooks

Reorganize and deduplicate pedagogical markdown in Jupyter notebooks.

Target: $ARGUMENTS

Arguments

• target: Notebook path, family name, or all
• --dry-run: List problems without modifying
• --aggressive: Aggressive deduplication
• --hierarchy-only: Fix heading structure only

Process

1. Parse target - Discover notebooks

2. For each notebook, launch a background agent:

   • Read notebook-cleaner agent instructions (.claude/agents/notebook-cleaner.md)
   • Read entire notebook, analyze structure
   • Identify problems (duplicates, misplaced cells, heading jumps, empty cells)
   • Fix via NotebookEdit (one operation at a time, verify diff after each)
   • Re-read notebook after each operation (indices change)

3. If --dry-run: List problems without modifying

4. Generate summary with cells deleted/modified per notebook

Common Issues

Pattern	Fix
Double introduction	Keep first, delete second
Orphan interpretation (before code)	Move after code cell
Heading jump (## then ####)	Change to ###
Empty transition cell	Delete or add content
Repeated concept definition	Keep best, delete others
Consecutive interpretation cells	Merge or delete duplicate

Safety Rules

• GOLDEN RULE: "Don't break what works" - if structure is good, don't modify
• Verify diffs after every operation
• Never delete code cells (only markdown)
• Re-read notebook after each edit (indices change)
• Use cell CONTENT for identification, not indices