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

Major Features:
- Hierarchical substudy system (like NX Solutions/Subcases)
  * Shared model files across all substudies
  * Independent configuration per substudy
  * Continuation support from previous substudies
  * Real-time incremental history updates
- Live history tracking with optimization_history_incremental.json
- Complete bracket_displacement_maximizing study with substudy examples

Core Fixes:
- Fixed expression update workflow to pass design_vars through simulation_runner
  * Restored working NX journal expression update mechanism
  * OP2 timestamp verification instead of file deletion
  * Resolved issue where all trials returned identical objective values
- Fixed LLMOptimizationRunner to pass design variables to simulation runner
- Enhanced NXSolver with timestamp-based file regeneration verification

New Components:
- optimization_engine/llm_optimization_runner.py - LLM-driven optimization runner
- optimization_engine/optimization_setup_wizard.py - Phase 3.3 setup wizard
- studies/bracket_displacement_maximizing/ - Complete substudy example
  * run_substudy.py - Substudy runner with continuation
  * run_optimization.py - Standalone optimization runner
  * config/substudy_template.json - Template for new substudies
  * substudies/coarse_exploration/ - 20-trial coarse search
  * substudies/fine_tuning/ - 50-trial refinement (continuation example)
  * SUBSTUDIES_README.md - Complete substudy documentation

Technical Improvements:
- Incremental history saving after each trial (optimization_history_incremental.json)
- Expression update workflow: .prt update → NX journal receives values → geometry update → FEM update → solve
- Trial indexing fix in substudy result saving
- Updated README with substudy system documentation

Testing:
- Successfully ran 20-trial coarse_exploration substudy
- Verified different objective values across trials (workflow fix validated)
- Confirmed live history updates in real-time
- Tested shared model file usage across substudies

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

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

.claude/settings.local.json

@@ -31,7 +31,24 @@
       "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_step_classifier.py)",
       "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_cbar_genetic_algorithm.py)",
       "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" -m pip install anthropic --quiet)",
-      "Bash(\"c:/Users/antoi/anaconda3/envs/atomizer/python.exe\" -m pip install anthropic --quiet)"
+      "Bash(\"c:/Users/antoi/anaconda3/envs/atomizer/python.exe\" -m pip install anthropic --quiet)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" optimization_engine/hook_generator.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" hook_weighted_objective_norm_stress_norm_disp.py test_input.json)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" optimization_engine/pynastran_research_agent.py)",
+      "Bash(git init:*)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" optimization_engine/extractor_orchestrator.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_phase_3_1_integration.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_bracket_llm_runner.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\":*)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_bracket_full_optimization.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/interactive_optimization_setup.py)",
+      "Bash(tee:*)",
+      "Bash(tree:*)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" tests/test_timestamp_verification.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" run_optimization.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" studies/bracket_displacement_maximizing/test_fix.py)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" run_substudy.py coarse_exploration)",
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" -c \"import json; h = json.load(open(''c:/Users/antoi/Documents/Atomaste/Atomizer/studies/bracket_displacement_maximizing/substudies/coarse_exploration/optimization_history_incremental.json'')); best = min(h, key=lambda x: x[''objective'']); print(f''Best Trial: {best[\"\"trial_number\"\"]}''); print(f''Parameters: tip={best[\"\"design_variables\"\"][\"\"tip_thickness\"\"]:.2f}mm, angle={best[\"\"design_variables\"\"][\"\"support_angle\"\"]:.2f}°''); print(f''Max Displacement: {best[\"\"results\"\"][\"\"max_displacement\"\"]:.6f}mm''); print(f''Objective: {best[\"\"objective\"\"]:.6f}'')\")"
     ],
     "deny": [],
     "ask": []