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The checkpoint command tracked 21 technical capability checkpoints, but this overlapped significantly with the milestones system which provides a more engaging, narrative-driven progress tracking experience. Changes: - Removed checkpoint command and test files - Updated milestone.py to remove checkpoint dependencies - Removed checkpoint integration from export.py, src.py, leaderboard.py - Updated CLI help text to reference milestones instead - Updated test suite (49/49 tests passing) - Archived checkpoint.py for reference Rationale: - Milestones is more engaging (historical ML achievements) - Module status already shows granular progress - Reduces duplication and confusion - Single clear progress tracking system 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>