clean up repository

[jeremymanning]

there are a bunch of notes and test files in the top-level directory. those should be deleted or migrated into the main pytest suite. we can also remove the notes directory. if there's anything relevant in any of the to-be-deleted markdown files, create github issues with that content before removing the files.

the scripts folder also has a bunch of tests that should either be removed or integrated into pytests.

in general: anything not related to the toolbox itself should be removed, while also backing up useful content in github issues or comments.

[jeremymanning]

✅ Resolved by Epic: clean-up-repository (#73)

This repository cleanup request has been fully completed through the comprehensive clean-up-repository epic (#73).

Original #72 Requirements vs Current Status:

✅ Notes Directory

• Request: Remove notes directory
• Status: ✅ COMPLETED - Directory removed as part of task Directory Removal #79

✅ Top-Level Test Files

• Request: Delete or migrate test files from root directory
• Status: ✅ COMPLETED - All test files migrated to organized tests/ structure via task Test File Migration #75

✅ Scripts Folder Cleanup

• Request: Remove or integrate tests from scripts folder
• Status: ✅ COMPLETED - Scripts reduced from 48 to 8 essential utilities via task Scripts Folder Cleanup #76

✅ Markdown File Cleanup

• Request: Remove irrelevant markdown files, preserve content in GitHub issues
• Status: ✅ COMPLETED - Content preserved via task Content Preservation Automation #74 (7 GitHub issues created), docs organized via task Documentation Consolidation #78

✅ Content Preservation

• Request: Back up useful content in GitHub issues before removal
• Status: ✅ COMPLETED - Automated content extraction via task Content Preservation Automation #74

Epic Results:

• 76MB repository size reduction (14% smaller)
• Clean Python project structure following best practices
• Organized test suite (unit/integration/real_world)
• Essential documentation preserved and organized
• All quality checks passing (black, flake8, pytest)

Epic Timeline: August 23-24, 2025
Tasks Completed: 10/10 (100% complete)
Repository Status: Clean, maintainable, standards-compliant

The repository cleanup is complete and exceeds the original requirements.

[jeremymanning]

📋 Comprehensive Repository Analysis Complete

After detailed review, the repository root contains 40+ extraneous files and directories that need cleanup:

Current Inventory:

• 14 Python scripts (debug_, check_, test utilities) - 30KB total
• 6 Jupyter notebooks (test notebooks) - 87KB total
• 9 config files (personal configs, generated files) - 350KB total
• 2 log files (aws logs, jupyter logs) - 135KB total
• 2 shell scripts (AWS setup scripts) - 6KB total
• 7 cache/build directories (build/, dist/, htmlcov/, etc.) - 200MB+ estimated
• 2 test environment directories (clustrix_test_env/, py310-test/)

Analysis Results:

✅ Parallel work streams identified for efficient cleanup
✅ Content preservation plan for valuable debugging insights
✅ File categorization complete (DELETE/MOVE/KEEP decisions)
✅ Estimated cleanup: 200MB+ repository size reduction

Next Steps:

The analysis shows this requires 4 parallel work streams:

• Stream A: Python script analysis & content extraction (3h)
• Stream B: Notebook & configuration cleanup (2.5h)
• Stream C: Directory & artifact removal (1.5h)
• Stream D: Documentation updates & prevention (1h)

Total effort: 8 hours work, 3 hours wall time with parallelization

Ready to start cleanup with: /pm:issue-start 72