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cleanup-notebooks

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

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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

PatternFix
Double introductionKeep first, delete second
Orphan interpretation (before code)Move after code cell
Heading jump (## then ####)Change to ###
Empty transition cellDelete or add content
Repeated concept definitionKeep best, delete others
Consecutive interpretation cellsMerge 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

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