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>

studies/bracket_displacement_maximizing/config/study_config.json

@@ -0,0 +1,81 @@
+{
+  "study_name": "bracket_displacement_maximizing",
+  "study_description": "Maximize displacement of bracket under load while maintaining safety factor >= 4.0",
+  "created_date": "2025-11-16",
+  "model": {
+    "part_file": "model/Bracket.prt",
+    "fem_file": "model/Bracket_fem1.fem",
+    "sim_file": "model/Bracket_sim1.sim",
+    "element_types": ["CHEXA", "CPENTA"],
+    "nodes": 585,
+    "elements": 316
+  },
+  "optimization": {
+    "objective": "Maximize displacement (minimize negative displacement)",
+    "direction": "minimize",
+    "algorithm": "TPE",
+    "n_trials": 20,
+    "design_variables": [
+      {
+        "name": "tip_thickness",
+        "type": "continuous",
+        "min": 15.0,
+        "max": 25.0,
+        "units": "mm",
+        "baseline": 17.0
+      },
+      {
+        "name": "support_angle",
+        "type": "continuous",
+        "min": 20.0,
+        "max": 40.0,
+        "units": "degrees",
+        "baseline": 38.0
+      }
+    ],
+    "constraints": [
+      {
+        "name": "safety_factor",
+        "type": ">=",
+        "value": 4.0,
+        "description": "Minimum safety factor constraint"
+      }
+    ]
+  },
+  "material": {
+    "name": "Aluminum 6061-T6",
+    "yield_strength": 276.0,
+    "yield_strength_units": "MPa",
+    "allowable_stress": 69.0,
+    "allowable_stress_units": "MPa"
+  },
+  "workflow": {
+    "phase": "3.3",
+    "wizard_validation": true,
+    "auto_element_detection": true,
+    "extractors": [
+      {
+        "action": "extract_displacement",
+        "result_type": "displacement"
+      },
+      {
+        "action": "extract_solid_stress",
+        "result_type": "stress",
+        "element_type": "auto-detected"
+      }
+    ],
+    "inline_calculations": [
+      {
+        "action": "calculate_safety_factor",
+        "formula": "276.0 / max_von_mises"
+      },
+      {
+        "action": "negate_displacement",
+        "formula": "-max_displacement"
+      }
+    ],
+    "hooks": [
+      "safety_factor_constraint"
+    ]
+  }
+}

studies/bracket_displacement_maximizing/config/substudy_template.json

@@ -0,0 +1,44 @@
+{
+  "substudy_name": "coarse_exploration",
+  "description": "Fast coarse exploration with wide parameter bounds",
+  "parent_study": "bracket_displacement_maximizing",
+  "created_date": "2025-11-16",
+
+  "optimization": {
+    "algorithm": "TPE",
+    "direction": "minimize",
+    "n_trials": 20,
+    "n_startup_trials": 10,
+    "design_variables": [
+      {
+        "parameter": "tip_thickness",
+        "type": "continuous",
+        "min": 15.0,
+        "max": 25.0,
+        "units": "mm"
+      },
+      {
+        "parameter": "support_angle",
+        "type": "continuous",
+        "min": 20.0,
+        "max": 40.0,
+        "units": "degrees"
+      }
+    ]
+  },
+
+  "continuation": {
+    "enabled": false,
+    "from_substudy": null,
+    "resume_from_trial": null,
+    "inherit_best_params": false
+  },
+
+  "solver": {
+    "nastran_version": "2412",
+    "use_journal": true,
+    "timeout": 300
+  },
+
+  "notes": "Template for creating new substudies"
+}