feat: Implement Study Organization System (Organization v2.0)

Reorganized simple_beam_optimization study and created templates for future
studies following best practices for clarity, chronology, and self-documentation.

## Study Reorganization (simple_beam_optimization)

**New Directory Structure**:
```
studies/simple_beam_optimization/
├── 1_setup/                    # Pre-optimization setup
│   ├── model/                  # Reference CAD/FEM model
│   └── benchmarking/           # Baseline validation results
├── 2_substudies/               # Optimization runs (numbered chronologically)
│   ├── 01_initial_exploration/
│   ├── 02_validation_3d_3trials/
│   ├── 03_validation_4d_3trials/
│   └── 04_full_optimization_50trials/
└── 3_reports/                  # Study-level analysis
    └── COMPREHENSIVE_BENCHMARK_RESULTS.md
```

**Key Changes**:
1. **Numbered Substudies**: 01_, 02_, 03_, 04_ indicate chronological order
2. **Reorganized Setup**: model/ and benchmarking/ moved to 1_setup/
3. **Centralized Reports**: Study-level docs moved to 3_reports/
4. **Substudy Documentation**: Each substudy has README.md explaining purpose/results

## Updated Metadata

**study_metadata.json** (v2.0):
- Tracks all 4 substudies with creation date, status, purpose
- Includes result summaries (best objective, feasible count)
- Documents new organization version

**Substudies Documented**:
- 01_initial_exploration - Initial design space exploration
- 02_validation_3d_3trials - Validate 3D parameter updates
- 03_validation_4d_3trials - Validate 4D updates including hole_count
- 04_full_optimization_50trials - Full 50-trial optimization

## Templates for Future Studies

**templates/study_template/** - Complete study structure:
- README.md template with study overview format
- study_metadata.json template with v2.0 schema
- Pre-created 1_setup/, 2_substudies/, 3_reports/ directories

**templates/substudy_README_template.md** - Standardized substudy documentation:
- Purpose and hypothesis
- Configuration changes from previous run
- Expected vs actual results
- Validation checklist
- Lessons learned
- Next steps

**templates/HOW_TO_CREATE_A_STUDY.md** - Complete guide:
- Quick start (9 steps from template to first run)
- Substudy workflow
- Directory structure reference
- Naming conventions
- Best practices
- Troubleshooting guide
- Examples

## Benefits

**Clarity**:
- Numbered substudies show chronological progression (01 → 02 → 03 → 04)
- Clear separation: setup vs. optimization runs vs. analysis
- Self-documenting via substudy READMEs

**Discoverability**:
- study_metadata.json provides complete substudy registry
- Each substudy README explains what was tested and why
- Easy to find results for specific runs

**Scalability**:
- Works for small studies (3 substudies) or large studies (50+)
- Chronological numbering scales to 99 substudies
- Template system makes new studies quick to set up

**Reproducibility**:
- Each substudy documents configuration changes
- Purpose and results clearly stated
- Lessons learned captured for future reference

## Implementation Details

**reorganize_study.py** - Migration script:
- Handles locked files gracefully
- Moves files to new structure
- Provides clear progress reporting
- Safe to run multiple times

**Organization Version**: 2.0
- Tracked in study_metadata.json
- Future studies will use this structure by default
- Existing studies can migrate or keep current structure

## Files Added

- templates/study_template/ - Complete study template
- templates/substudy_README_template.md - Substudy documentation template
- templates/HOW_TO_CREATE_A_STUDY.md - Comprehensive creation guide
- reorganize_study.py - Migration script for existing studies

## Files Reorganized (simple_beam_optimization)

**Moved to 1_setup/**:
- model/ → 1_setup/model/ (CAD/FEM reference files)
- substudies/benchmarking/ → 1_setup/benchmarking/
- baseline_validation.json → 1_setup/

**Renamed and Moved to 2_substudies/**:
- substudies/initial_exploration/ → 2_substudies/01_initial_exploration/
- substudies/validation_3trials/ → 2_substudies/02_validation_3d_3trials/
- substudies/validation_4d_3trials/ → 2_substudies/03_validation_4d_3trials/
- substudies/full_optimization_50trials/ → 2_substudies/04_full_optimization_50trials/

**Moved to 3_reports/**:
- COMPREHENSIVE_BENCHMARK_RESULTS.md → 3_reports/

**Substudy-Specific Docs** (moved to substudy directories):
- OPTIMIZATION_RESULTS_50TRIALS.md → 2_substudies/04_full_optimization_50trials/OPTIMIZATION_RESULTS.md

## Documentation Created

Each substudy now has README.md documenting:
- **01_initial_exploration**: Initial exploration purpose
- **02_validation_3d_3trials**: 3D parameter update validation
- **03_validation_4d_3trials**: hole_count validation success
- **04_full_optimization_50trials**: Full results, no feasible designs found

## Next Steps

**For Future Studies**:
1. Copy templates/study_template/
2. Follow templates/HOW_TO_CREATE_A_STUDY.md
3. Use numbered substudies (01_, 02_, ...)
4. Document each substudy with README.md

**For Existing Studies**:
- Can migrate using reorganize_study.py
- Or apply organization v2.0 to new substudies only
- See docs/STUDY_ORGANIZATION.md for migration guide

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

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

studies/simple_beam_optimization/1_setup/benchmarking/BENCHMARK_REPORT.md

@@ -0,0 +1,99 @@
+# Benchmarking Report
+
+**Study**: simple_beam_optimization
+**Date**: 2025-11-17T11:18:28.329069
+**Validation**: ✅ PASSED
+
+## Model Introspection
+
+**Expressions Found**: 30
+
+| Expression | Value | Units |
+|------------|-------|-------|
+| Pattern_p7 | None |  |
+| Pattern_p8 | 444.444444444444 | MilliMeter |
+| Pattern_p9 | None | MilliMeter |
+| Pattern_p10 | 1.0 |  |
+| Pattern_p11 | 10.0 | MilliMeter |
+| Pattern_p12 | 0.0 | MilliMeter |
+| beam_face_thickness | 20.0 | MilliMeter |
+| beam_half_core_thickness | 20.0 | MilliMeter |
+| beam_half_height | 250.0 | MilliMeter |
+| beam_half_width | 150.0 | MilliMeter |
+| beam_lenght | 5000.0 | MilliMeter |
+| hole_count | 10.0 |  |
+| holes_diameter | 300.0 | MilliMeter |
+| p4 | None | MilliMeter |
+| p5 | 0.0 | MilliMeter |
+| p6 | 4000.0 | MilliMeter |
+| p13 | 0.0 | Degrees |
+| p19 | 4000.0 | MilliMeter |
+| p34 | 4000.0 | MilliMeter |
+| p50 | 4000.0 | MilliMeter |
+| p119 | 4000.0 | MilliMeter |
+| p130 | 10.0 |  |
+| p132 | 444.444444444444 | MilliMeter |
+| p134 | 4000.0 | MilliMeter |
+| p135 | 4000.0 | MilliMeter |
+| p137 | 1.0 |  |
+| p139 | 10.0 | MilliMeter |
+| p141 | 0.0 | MilliMeter |
+| p143 | 0.0 | Degrees |
+| p173 | 973.968443678471 | Kilogram |
+
+## OP2 Analysis
+
+- **Element Types**: CQUAD4
+- **Result Types**: displacement, stress
+- **Subcases**: [1]
+- **Nodes**: 0
+- **Elements**: 0
+
+## Baseline Performance
+
+*No baseline results extracted*
+
+## Configuration Proposals
+
+### Proposed Design Variables
+
+- **Pattern_p7**: ±20% of None 
+- **Pattern_p8**: ±20% of 444.444444444444 MilliMeter
+- **Pattern_p9**: ±20% of None MilliMeter
+- **Pattern_p10**: ±20% of 1.0 
+- **Pattern_p11**: ±20% of 10.0 MilliMeter
+- **Pattern_p12**: ±20% of 0.0 MilliMeter
+- **beam_face_thickness**: ±20% of 20.0 MilliMeter
+- **beam_half_core_thickness**: ±20% of 20.0 MilliMeter
+- **beam_half_height**: ±20% of 250.0 MilliMeter
+- **beam_half_width**: ±20% of 150.0 MilliMeter
+- **beam_lenght**: ±20% of 5000.0 MilliMeter
+- **hole_count**: ±20% of 10.0 
+- **holes_diameter**: ±20% of 300.0 MilliMeter
+- **p4**: ±20% of None MilliMeter
+- **p5**: ±20% of 0.0 MilliMeter
+- **p6**: ±20% of 4000.0 MilliMeter
+- **p13**: ±20% of 0.0 Degrees
+- **p19**: ±20% of 4000.0 MilliMeter
+- **p34**: ±20% of 4000.0 MilliMeter
+- **p50**: ±20% of 4000.0 MilliMeter
+- **p119**: ±20% of 4000.0 MilliMeter
+- **p130**: ±20% of 10.0 
+- **p132**: ±20% of 444.444444444444 MilliMeter
+- **p134**: ±20% of 4000.0 MilliMeter
+- **p135**: ±20% of 4000.0 MilliMeter
+- **p137**: ±20% of 1.0 
+- **p139**: ±20% of 10.0 MilliMeter
+- **p141**: ±20% of 0.0 MilliMeter
+- **p143**: ±20% of 0.0 Degrees
+- **p173**: ±20% of 973.968443678471 Kilogram
+
+### Proposed Extractors
+
+- **extract_displacement**: Extract displacement results from OP2 file
+- **extract_solid_stress**: Extract stress from CQUAD4 elements
+
+### Proposed Objectives
+
+- max_displacement (minimize or maximize)
+- max_von_mises (minimize for safety)