Antoine d1261d62fd refactor: Major project cleanup and reorganization ...

## Removed Duplicate Directories
- Deleted old `dashboard/` (replaced by atomizer-dashboard)
- Deleted old `mcp_server/` Python tools (moved model_discovery to optimization_engine)
- Deleted `tests/mcp_server/` (obsolete tests)
- Deleted `launch_dashboard.bat` (old launcher)

## Consolidated Code
- Moved `mcp_server/tools/model_discovery.py` to `optimization_engine/model_discovery/`
- Updated import in `optimization_config_builder.py`
- Deleted stub `extract_mass.py` (use extract_mass_from_bdf instead)
- Deleted unused `intelligent_setup.py` and `hybrid_study_creator.py`
- Archived `result_extractors/` to `archive/deprecated/`

## Documentation Cleanup
- Deleted deprecated `docs/06_PROTOCOLS_DETAILED/` (14 files)
- Archived dated dev docs to `docs/08_ARCHIVE/sessions/`
- Archived old plans to `docs/08_ARCHIVE/plans/`
- Updated `docs/protocols/README.md` with SYS_15

## Skills Consolidation
- Archived redundant study creation skills to `.claude/skills/archive/`
- Kept `core/study-creation-core.md` as canonical

## Housekeeping
- Updated `.gitignore` to prevent `nul` and `_dat_run*.dat`

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2025-12-12 11:24:02 -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

__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

demo_research_agent.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

interactive_optimization_setup.py

feat: Add substudy system with live history tracking and workflow fixes

2025-11-16 21:29:54 -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

docs: Reorganize documentation structure

2025-11-16 08:40:53 -05:00

run_beam_benchmarking_clean.py

fix: Remove redundant save() call that overwrote NX expression updates

2025-11-17 21:24:02 -05:00

run_beam_benchmarking.py

fix: Remove redundant save() call that overwrote NX expression updates

2025-11-17 21:24:02 -05:00

run_benchmarking_simple.py

fix: Remove redundant save() call that overwrote NX expression updates

2025-11-17 21:24:02 -05:00

setup_beam_optimization.py

fix: Remove redundant save() call that overwrote NX expression updates

2025-11-17 21:24:02 -05:00

test_api_verification.py

test: Add API verification test with hardcoded key for periodic checks

2025-11-17 09:27:52 -05:00

test_beam_workflow.py

fix: Remove redundant save() call that overwrote NX expression updates

2025-11-17 21:24:02 -05:00

test_bracket_full_optimization.py

feat: Add substudy system with live history tracking and workflow fixes

2025-11-16 21:29:54 -05:00

test_bracket_llm_runner.py

feat: Add substudy system with live history tracking and workflow fixes

2025-11-16 21:29:54 -05:00

test_cbar_genetic_algorithm.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_cbush_optimization.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_code_generation.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_complete_research_workflow.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_complex_multiobj_request.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_hooks_with_bracket.py

docs: Reorganize documentation structure

2025-11-16 08:40:53 -05:00

test_interactive_session.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_journal_optimization.py

docs: Reorganize documentation structure

2025-11-16 08:40:53 -05:00

test_knowledge_base_search.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -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

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_llm_runner_init.py

feat: Add substudy system with live history tracking and workflow fixes

2025-11-16 21:29:54 -05:00

test_modal_deformation_request.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -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

feat: Add substudy system with live history tracking and workflow fixes

2025-11-16 21:29:54 -05:00

test_phase_2_5_intelligent_gap_detection.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -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

feat: Phase 3.2 Task 1.2 - Wire LLMOptimizationRunner to production

2025-11-17 20:48:40 -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

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_step_classifier.py

feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis

2025-11-16 13:35:41 -05:00

test_task_1_2_integration.py

feat: Phase 3.2 Task 1.2 - Wire LLMOptimizationRunner to production

2025-11-17 20:48:40 -05:00

test_timestamp_verification.py

feat: Add substudy system with live history tracking and workflow fixes

2025-11-16 21:29:54 -05:00

test_training_data_exporter.py

feat: Add AtomizerField training data export and intelligent model discovery

2025-11-26 12:01:50 -05:00

verify_parametric_link.py

feat: Implement complete FEM regeneration workflow

2025-11-15 12:43:31 -05:00