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>

templates/study_template/README.md

@@ -0,0 +1,72 @@
+# [Study Name]
+
+**Created**: YYYY-MM-DD
+**Status**: [planned | active | completed | archived]
+
+## Overview
+
+[Brief description of what this study aims to achieve]
+
+## Design Problem
+
+**Part**: [Part name/description]
+**Goal**: [What are we trying to optimize?]
+**Constraints**: [What limits must be respected?]
+
+## Design Variables
+
+| Variable | Type | Min | Max | Units | Description |
+|----------|------|-----|-----|-------|-------------|
+| var1_name | continuous | X.X | Y.Y | mm | Description |
+| var2_name | integer | N | M | - | Description |
+
+## Objectives
+
+1. **Primary Objective**: [Main goal - e.g., minimize displacement]
+2. **Secondary Objectives**: [Additional goals - e.g., minimize mass, stress]
+
+## Constraints
+
+- **Constraint 1**: [Description and limit - e.g., max displacement < 10mm]
+- **Constraint 2**: [Description and limit]
+
+## Study Organization
+
+### 1_setup/
+Pre-optimization setup and validation
+- `model/` - Reference CAD/FEM model
+- `benchmarking/` - Baseline validation results
+
+### 2_substudies/
+Optimization runs (numbered chronologically)
+- `01_[descriptive_name]/` - First substudy
+- `02_[descriptive_name]/` - Second substudy
+- ...
+
+### 3_reports/
+Study-level analysis and comparisons
+- Cross-substudy comparisons
+- Final recommendations
+- Lessons learned
+
+## Current Status
+
+**Last Updated**: YYYY-MM-DD
+
+**Completed Substudies**: N
+**Total Trials Run**: XXX
+**Best Result So Far**: [Brief summary]
+
+**Next Steps**:
+- [ ] Step 1
+- [ ] Step 2
+
+## Key Findings
+
+[Summary of important discoveries]
+
+## References
+
+- Configuration: [beam_optimization_config.json](beam_optimization_config.json)
+- Metadata: [study_metadata.json](study_metadata.json)
+- Runner Script: [run_optimization.py](run_optimization.py)

templates/study_template/study_metadata.json

@@ -0,0 +1,25 @@
+{
+  "study_name": "your_study_name",
+  "description": "Brief description of what this study optimizes",
+  "created": "YYYY-MM-DDTHH:MM:SS",
+  "status": "planned",
+  "design_variables": [
+    "variable_name_1",
+    "variable_name_2"
+  ],
+  "objectives": [
+    "objective_name_1",
+    "objective_name_2"
+  ],
+  "constraints": [
+    "constraint_name_1"
+  ],
+  "substudies": [],
+  "last_modified": "YYYY-MM-DDTHH:MM:SS",
+  "organization_version": "2.0",
+  "directory_structure": {
+    "1_setup": "Pre-optimization setup (model, benchmarking)",
+    "2_substudies": "Optimization runs (numbered chronologically)",
+    "3_reports": "Study-level comparative analysis"
+  }
+}