feat: Add MLP surrogate with Turbo Mode for 100x faster optimization

Neural Acceleration (MLP Surrogate):
- Add run_nn_optimization.py with hybrid FEA/NN workflow
- MLP architecture: 4-layer (64->128->128->64) with BatchNorm/Dropout
- Three workflow modes:
  - --all: Sequential export->train->optimize->validate
  - --hybrid-loop: Iterative Train->NN->Validate->Retrain cycle
  - --turbo: Aggressive single-best validation (RECOMMENDED)
- Turbo mode: 5000 NN trials + 50 FEA validations in ~12 minutes
- Separate nn_study.db to avoid overloading dashboard

Performance Results (bracket_pareto_3obj study):
- NN prediction errors: mass 1-5%, stress 1-4%, stiffness 5-15%
- Found minimum mass designs at boundary (angle~30deg, thick~30mm)
- 100x speedup vs pure FEA exploration

Protocol Operating System:
- Add .claude/skills/ with Bootstrap, Cheatsheet, Context Loader
- Add docs/protocols/ with operations (OP_01-06) and system (SYS_10-14)
- Update SYS_14_NEURAL_ACCELERATION.md with MLP Turbo Mode docs

NX Automation:
- Add optimization_engine/hooks/ for NX CAD/CAE automation
- Add study_wizard.py for guided study creation
- Fix FEM mesh update: load idealized part before UpdateFemodel()

New Study:
- bracket_pareto_3obj: 3-objective Pareto (mass, stress, stiffness)
- 167 FEA trials + 5000 NN trials completed
- Demonstrates full hybrid workflow

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

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

studies/bracket_pareto_3obj/README.md

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+# bracket_pareto_3obj
+
+Three-objective Pareto optimization: minimize mass, minimize stress, maximize stiffness
+
+**Generated**: 2025-12-06 14:43
+**Protocol**: Multi-Objective NSGA-II
+**Trials**: 100
+
+---
+
+## 1. Engineering Problem
+
+Three-objective Pareto optimization: minimize mass, minimize stress, maximize stiffness
+
+---
+
+## 2. Mathematical Formulation
+
+### Design Variables
+
+| Parameter | Bounds | Units | Description |
+|-----------|--------|-------|-------------|
+| `support_angle` | [20, 70] | degrees | Angle of support arm relative to base |
+| `tip_thickness` | [30, 60] | mm | Thickness at bracket tip where load is applied |
+
+
+### Objectives
+
+| Objective | Goal | Extractor | Weight |
+|-----------|------|-----------|--------|
+| mass | minimize | `extract_mass_from_bdf` | 1.0 |
+| stress | minimize | `extract_solid_stress` | 1.0 |
+| stiffness | maximize | `extract_displacement` | 1.0 |
+
+
+### Constraints
+
+| Constraint | Type | Threshold | Units |
+|------------|------|-----------|-------|
+| stress_limit | less_than | 300 | MPa |
+
+
+---
+
+## 3. Optimization Algorithm
+
+- **Protocol**: protocol_11_multi
+- **Sampler**: NSGAIISampler
+- **Trials**: 100
+- **Neural Acceleration**: Disabled
+
+---
+
+## 4. Simulation Pipeline
+
+```
+Design Variables → NX Expression Update → Nastran Solve → Result Extraction → Objective Evaluation
+```
+
+---
+
+## 5. Result Extraction Methods
+
+| Result | Extractor | Source |
+|--------|-----------|--------|
+| mass | `extract_mass_from_bdf` | OP2/DAT |
+| stress | `extract_solid_stress` | OP2/DAT |
+| stiffness | `extract_displacement` | OP2/DAT |
+
+---
+
+## 6. Study File Structure
+
+```
+bracket_pareto_3obj/
+├── 1_setup/
+│   ├── model/
+│   │   ├── Bracket.prt
+│   │   ├── Bracket_sim1.sim
+│   │   └── Bracket_fem1.fem
+│   ├── optimization_config.json
+│   └── workflow_config.json
+├── 2_results/
+│   ├── study.db
+│   └── optimization.log
+├── run_optimization.py
+├── reset_study.py
+├── README.md
+├── STUDY_REPORT.md
+└── MODEL_INTROSPECTION.md
+```
+
+---
+
+## 7. Quick Start
+
+```bash
+# 1. Discover model outputs
+python run_optimization.py --discover
+
+# 2. Validate setup with single trial
+python run_optimization.py --validate
+
+# 3. Run integration test (3 trials)
+python run_optimization.py --test
+
+# 4. Run full optimization
+python run_optimization.py --run --trials 100
+
+# 5. Resume if interrupted
+python run_optimization.py --run --trials 50 --resume
+```
+
+---
+
+## 8. Results Location
+
+| File | Description |
+|------|-------------|
+| `2_results/study.db` | Optuna SQLite database |
+| `2_results/optimization.log` | Structured log file |
+| `2_results/pareto_front.json` | Pareto-optimal solutions |
+
+---
+
+## 9. References
+
+- [Atomizer Documentation](../../docs/)
+- [Protocol protocol_11_multi](../../docs/protocols/system/)
+- [Extractor Library](../../docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md)