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>

tests/bracket_sim1-solution_1.dat

@@ -3,15 +3,15 @@ $*
 $*                    Simcenter v2412.0.0.3001 Translator
 $*                    for Simcenter Nastran version 2412.0
 $*
-$*             FEM FILE: C:\Users\antoi\Documents\Atomaste\Atomizer\tests\Bracket_fem1.fem
-$*             SIM FILE: C:\Users\antoi\Documents\Atomaste\Atomizer\tests\Bracket_sim1.sim
+$*             FEM FILE: c:\Users\antoi\Documents\Atomaste\Atomizer\tests\Bracket_fem1.fem
+$*             SIM FILE: c:\Users\antoi\Documents\Atomaste\Atomizer\tests\Bracket_sim1.sim
 $*        ANALYSIS TYPE: Structural
 $*        SOLUTION NAME: Solution 1
 $*        SOLUTION TYPE: SOL 101 Linear Statics
 $*
 $*    SOLVER INPUT FILE: bracket_sim1-solution_1.dat
-$*        CREATION DATE: 15-Nov-2025
-$*        CREATION TIME: 12:17:41
+$*        CREATION DATE: 16-Nov-2025
+$*        CREATION TIME: 20:44:27
 $*             HOSTNAME: AntoineThinkpad
 $*      NASTRAN LICENSE: Desktop Bundle
 $*