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/substudies/fine_tuning/config.json

@@ -0,0 +1,36 @@
+{
+  "substudy_name": "fine_tuning",
+  "description": "Fine-grained optimization with 50 trials in narrow bounds around best design from coarse exploration",
+  "parent_study": "bracket_displacement_maximizing",
+  "created_date": "2025-11-16",
+
+  "optimization": {
+    "algorithm": "TPE",
+    "direction": "minimize",
+    "n_trials": 50,
+    "n_startup_trials": 5,
+    "design_variables": [
+      {
+        "parameter": "tip_thickness",
+        "min": 18.0,
+        "max": 22.0,
+        "units": "mm",
+        "comment": "Narrowed from coarse_exploration results"
+      },
+      {
+        "parameter": "support_angle",
+        "min": 28.0,
+        "max": 35.0,
+        "units": "degrees",
+        "comment": "Narrowed from coarse_exploration results"
+      }
+    ]
+  },
+
+  "continuation": {
+    "enabled": true,
+    "from_substudy": "coarse_exploration",
+    "inherit_best_params": true,
+    "comment": "Start from best design found in coarse exploration"
+  }
+}