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Anto01 a3f18dc377 chore: Project cleanup and Canvas UX improvements (Phase 7-9) 
## Cleanup (v0.5.0)
- Delete 102+ orphaned MCP session temp files
- Remove build artifacts (htmlcov, dist, __pycache__)
- Archive superseded plan docs (RALPH_LOOP V2/V3, CANVAS V3, etc.)
- Move debug/analysis scripts from tests/ to tools/analysis/
- Archive redundant NX journals to archive/nx_journals/
- Archive monolithic PROTOCOL.md to docs/archive/
- Update .gitignore with missing patterns
- Clean old study files (optimization_log_old.txt, run_optimization_old.py)

## Canvas UX (Phases 7-9)
- Phase 7: Resizable panels with localStorage persistence
  - Left sidebar: 200-400px, Right panel: 280-600px
  - New useResizablePanel hook and ResizeHandle component
- Phase 8: Enable all palette items
  - All 8 node types now draggable
  - Singleton logic for model/solver/algorithm/surrogate
- Phase 9: Solver configuration
  - Add SolverEngine type (nxnastran, mscnastran, python, etc.)
  - Add NastranSolutionType (SOL101-SOL200)
  - Engine/solution dropdowns in config panel
  - Python script path support

## Documentation
- Update CHANGELOG.md with recent versions
- Update docs/00_INDEX.md
- Create examples/README.md
- Add docs/plans/CANVAS_UX_IMPROVEMENTS.md
2026-01-24 15:17:34 -05:00
..
interview
feat: Implement Study Interview Mode as default study creation method
2026-01-03 11:06:07 -05:00
test_output/task_1_2_integration/generated_hooks
fix: Remove redundant save() call that overwrote NX expression updates
2025-11-17 21:24:02 -05:00
unit
refactor: Reorganize code structure and create tests directory
2026-01-07 09:01:37 -05:00
__init__.py
feat: Implement Option A - MCP Model Discovery tool
2025-11-15 13:23:05 +00:00
Bracket_fem1_i.prt
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
Bracket_fem1.fem
feat: Update model discovery to handle real binary NX files
2025-11-15 13:44:42 +00:00
bracket_sim1-solution_1.dat
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
bracket_sim1-solution_1.t13980_32.asg
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
Bracket_sim1.sim
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
Bracket.prt
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
conftest.py
refactor: Reorganize code structure and create tests directory
2026-01-07 09:01:37 -05:00
demo_research_agent.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
interactive_optimization_setup.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
journal_apply_expression.py
fix: Apply expression updates directly in NX journal
2025-11-15 12:47:55 -05:00
journal_open_run_sim_and_save.py
feat: Add journal-based NX solver integration for optimization
2025-11-15 12:23:57 -05:00
journal_open_run_sim.py
feat: Add journal-based NX solver integration for optimization
2025-11-15 12:23:57 -05:00
journal_reload_master.py
feat: Add journal-based NX solver integration for optimization
2025-11-15 12:23:57 -05:00
journal_with_regenerate.py
feat: Implement complete FEM regeneration workflow
2025-11-15 12:43:31 -05:00
run_5trial_test.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
run_beam_benchmarking_clean.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
run_beam_benchmarking.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
run_benchmarking_simple.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
setup_beam_optimization.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_api_verification.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_beam_workflow.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_bracket_full_optimization.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_bracket_llm_runner.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_cbar_genetic_algorithm.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_cbush_optimization.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_code_generation.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_complete_research_workflow.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_complex_multiobj_request.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_context_engineering.py
feat: Implement ACE Context Engineering framework (SYS_17)
2025-12-29 20:21:20 -05:00
test_context_integration.py
feat: Implement ACE Context Engineering framework (SYS_17)
2025-12-29 20:21:20 -05:00
test_e2e_unified_config.py
feat(config): AtomizerSpec v2.0 Pydantic models, validators, and tests
2026-01-20 13:12:03 -05:00
test_hooks_with_bracket.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_insights_import.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_interactive_session.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_journal_optimization.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_knowledge_base_search.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_lifecycle_hook_integration.py
feat: Complete Phase 3 - pyNastran Documentation Integration
2025-11-16 16:33:48 -05:00
test_llm_complex_request.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_llm_runner_init.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_mcp_tools.py
feat(config): AtomizerSpec v2.0 Pydantic models, validators, and tests
2026-01-20 13:12:03 -05:00
test_migrator.py
feat(config): AtomizerSpec v2.0 Pydantic models, validators, and tests
2026-01-20 13:12:03 -05:00
test_modal_deformation_request.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_nxopen_intellisense.py
fix: Update intellisense test to prevent execution errors
2025-11-17 08:57:08 -05:00
test_optimization_setup_wizard.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_phase_2_5_intelligent_gap_detection.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_phase_3_1_integration.py
feat: Complete Phase 3.1 - Extractor Orchestration & End-to-End Automation
2025-11-16 19:39:04 -05:00
test_phase_3_2_e2e.py
refactor: Implement centralized extractor library to eliminate code duplication
2025-11-18 09:00:10 -05:00
test_phase_3_2_llm_mode.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_plugin_system.py
feat: Implement Phase 1 - Plugin & Hook System
2025-11-15 14:46:49 -05:00
test_research_agent.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_spec_api.py
feat(config): AtomizerSpec v2.0 Pydantic models, validators, and tests
2026-01-20 13:12:03 -05:00
test_spec_manager.py
feat(config): AtomizerSpec v2.0 Pydantic models, validators, and tests
2026-01-20 13:12:03 -05:00
test_step_classifier.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_task_1_2_integration.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_timestamp_verification.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_training_data_exporter.py
refactor: Major reorganization of optimization_engine module structure
2025-12-29 12:30:59 -05:00
test_zernike_import.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_zernike_insight.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_zernike_methods_comparison.py
feat: Add OPD method support to Zernike visualization with Standard/OPD toggle
2025-12-22 21:03:19 -05:00
test_zernike_opd_comparison.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_zernike_opd_with_prescription.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
verify_parametric_link.py
feat: Implement complete FEM regeneration workflow
2025-11-15 12:43:31 -05:00