chore: Second cleanup wave - organize root directory
- Archive: 85 agent .txt files → docs/archive/agents/legacy_txt/
- Scripts: Move 110 shell scripts → scripts/ (keep deploy.sh in root)
- Models: Move 18 .safetensors → ml/models/checkpoints/training_artifacts/
- Delete: 34 directories (~33GB freed) - target/, coverage_*, test artifacts
- Build: Clean 14 build artifacts (.rlib, .o, .pid, binaries)
- Tests: Move 14 .rs files → tests/standalone/
- SQL: Move 5 files → sql/ (keep init-db*.sql for Docker)
- Wave 153: Archive to docs/archive/historical/wave153/
- Docs: Archive 9 markdown files to wave_d/reports/ and historical/
Total impact: ~34GB freed (both waves), root directory cleaned from 583 to ~40 essential files
Directory count reduced from 65 to 31 (52% reduction)
All historical data preserved in organized archive structure
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