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Test Cleanup (113 files, -22,000 lines): - Remove 21 redundant run_all_tests.py files - Remove checkpoints/ folder (22 obsolete checkpoint files) - Remove progressive/, debugging/, diagnostic/ folders - Remove duplicate integration tests and examples - Remove orphaned dev artifacts and generated outputs - Consolidate test_gradient_flow_overall.py into system/ Documentation Cleanup (4 files removed): - Remove duplicate HOW_TO_USE.md, WORKFLOW.md, SYSTEM_DESIGN.md - Trim environment/README.md from 334 to 86 lines - Update capstone/README.md removing outdated bug references Test Fixes: - Add requires_grad=True to layer parameters in gradient tests - Fix PositionalEncoding argument order in test_shapes.py - Adjust performance thresholds for realistic expectations - Fix gradient clipping to handle memoryview correctly - Update zero_grad assertions to accept None or zeros