docs: Add GitHub setup and development guides

DEVELOPMENT.md

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+# Development Guide
+
+## Project Setup Complete! ✅
+
+Your NX OptiMaster project has been initialized with the following structure:
+
+```
+C:\Users\antoi\Documents\Atomaste\Atomizer\
+├── .git/                           # Git repository
+├── .gitignore                      # Ignore patterns
+├── LICENSE                         # Proprietary license
+├── README.md                       # Main documentation
+├── GITHUB_SETUP.md                 # GitHub push instructions
+├── DEVELOPMENT.md                  # This file
+├── pyproject.toml                  # Python package configuration
+├── requirements.txt                # Pip dependencies
+│
+├── config/                         # Configuration templates
+│   ├── nx_config.json.template
+│   └── optimization_config_template.json
+│
+├── mcp_server/                     # MCP Server (Phase 1)
+│   ├── __init__.py
+│   ├── tools/                      # MCP tool implementations
+│   │   └── __init__.py
+│   ├── schemas/                    # JSON schemas for validation
+│   └── prompts/                    # LLM system prompts
+│       └── examples/               # Few-shot examples
+│
+├── optimization_engine/            # Core optimization (Phase 4)
+│   ├── __init__.py
+│   └── result_extractors/          # Pluggable metric extractors
+│       └── __init__.py             # Base classes + registry
+│
+├── nx_journals/                    # NXOpen scripts (Phase 3)
+│   ├── __init__.py
+│   └── utils/                      # Helper functions
+│
+├── dashboard/                      # Web UI (Phase 2)
+│   ├── frontend/                   # React app
+│   └── backend/                    # FastAPI server
+│
+├── tests/                          # Unit tests
+├── docs/                           # Documentation
+└── examples/                       # Example projects
+```
+
+## Current Status: Phase 0 - Foundation ✅
+
+- [x] Project structure created
+- [x] Git repository initialized
+- [x] Python package configuration
+- [x] License and documentation
+- [x] Initial commit ready
+
+## Next Development Phases
+
+### 🎯 Immediate Next Steps (Choose One)
+
+#### Option A: Start with MCP Server (Recommended)
+**Goal**: Get conversational FEA model discovery working
+
+1. **Implement `discover_fea_model` tool**:
+   ```bash
+   # Create the tool
+   touch mcp_server/tools/model_discovery.py
+   ```
+
+   - Parse .sim files to extract solutions, expressions, FEM info
+   - Use existing Atomizer patterns from your P04 project
+   - Return structured JSON for LLM consumption
+
+2. **Set up MCP server skeleton**:
+   ```bash
+   # Install MCP SDK
+   pip install mcp
+
+   # Create server entry point
+   touch mcp_server/server.py
+   ```
+
+3. **Test with a real .sim file**:
+   - Point it to one of your existing models
+   - Verify it extracts expressions correctly
+
+#### Option B: Port Atomizer Optimization Engine
+**Goal**: Get core optimization working independently
+
+1. **Copy Atomizer modules**:
+   ```bash
+   # From your P04/Atomizer project, copy:
+   cp ../Projects/P04/Atomizer/code/multi_optimizer.py optimization_engine/
+   cp ../Projects/P04/Atomizer/code/config_loader.py optimization_engine/
+   cp ../Projects/P04/Atomizer/code/surrogate_optimizer.py optimization_engine/
+   ```
+
+2. **Adapt for general use**:
+   - Remove Zernike-specific code
+   - Generalize result extraction to use plugin system
+   - Update import paths
+
+3. **Create a simple test**:
+   ```python
+   # tests/test_optimizer.py
+   def test_basic_optimization():
+       config = load_config("config/optimization_config_template.json")
+       optimizer = MultiParameterOptimizer(config)
+       # ...
+   ```
+
+#### Option C: Build Dashboard First
+**Goal**: Get real-time monitoring UI working
+
+1. **Set up React frontend**:
+   ```bash
+   cd dashboard/frontend
+   npx create-react-app . --template typescript
+   npm install plotly.js recharts
+   ```
+
+2. **Set up FastAPI backend**:
+   ```bash
+   cd dashboard/backend
+   touch server.py
+   # Implement WebSocket endpoint for live updates
+   ```
+
+3. **Create mock data endpoint**:
+   - Serve fake optimization history
+   - Test plots and visualizations
+
+## Recommended Workflow: Iterative Development
+
+### Week 1: MCP + Model Discovery
+- Implement `discover_fea_model` tool
+- Test with real .sim files
+- Get LLM integration working
+
+### Week 2: Optimization Engine Port
+- Copy and adapt Atomizer core modules
+- Create pluggable result extractors
+- Test with simple optimization
+
+### Week 3: NXOpen Bridge
+- Build file-based communication
+- Create generic journal dispatcher
+- Test expression updates
+
+### Week 4: Dashboard MVP
+- React frontend skeleton
+- FastAPI backend with WebSocket
+- Real-time iteration monitoring
+
+## Development Commands
+
+### Python Environment
+
+```bash
+# Create conda environment
+conda create -n nx-optimaster python=3.10
+conda activate nx-optimaster
+
+# Install in development mode
+pip install -e .
+
+# Install dev dependencies
+pip install -e ".[dev]"
+```
+
+### Testing
+
+```bash
+# Run all tests
+pytest
+
+# With coverage
+pytest --cov=mcp_server --cov=optimization_engine
+
+# Run specific test
+pytest tests/test_model_discovery.py -v
+```
+
+### Code Quality
+
+```bash
+# Format code
+black .
+
+# Lint
+ruff check .
+
+# Type checking
+mypy mcp_server optimization_engine
+```
+
+### Git Workflow
+
+```bash
+# Create feature branch
+git checkout -b feature/model-discovery
+
+# Make changes, test, commit
+git add .
+git commit -m "feat: implement FEA model discovery tool"
+
+# Push to GitHub
+git push -u origin feature/model-discovery
+
+# Merge to main
+git checkout main
+git merge feature/model-discovery
+git push origin main
+```
+
+## Integration with Existing Atomizer
+
+Your existing Atomizer project is at:
+```
+C:\Users\antoi\Documents\Atomaste\Projects\P04\Atomizer\
+```
+
+You can reference and copy modules from there as needed. Key files to adapt:
+
+| Atomizer File | New Location | Adaptation Needed |
+|--------------|--------------|-------------------|
+| `code/multi_optimizer.py` | `optimization_engine/multi_optimizer.py` | Minimal - works as-is |
+| `code/config_loader.py` | `optimization_engine/config_loader.py` | Extend schema for extractors |
+| `code/zernike_Post_Script_NX.py` | `optimization_engine/result_extractors/zernike.py` | Convert to plugin class |
+| `code/journal_NX_Update_and_Solve.py` | `nx_journals/update_and_solve.py` | Generalize for any .sim |
+| `code/nx_post_each_iter.py` | `nx_journals/post_process.py` | Use extractor registry |
+
+## Useful Resources
+
+- **Optuna Docs**: https://optuna.readthedocs.io/
+- **NXOpen API**: https://docs.sw.siemens.com/en-US/doc/209349590/
+- **MCP Protocol**: https://modelcontextprotocol.io/
+- **FastAPI**: https://fastapi.tiangolo.com/
+- **React + TypeScript**: https://react-typescript-cheatsheet.netlify.app/
+
+## Questions to Consider
+
+Before starting development, decide on:
+
+1. **Which phase to tackle first?** (MCP, Engine, Dashboard, or NXOpen)
+2. **Target NX version?** (2306, 2406, or multi-version support)
+3. **Deployment strategy?** (Local only or client-server architecture)
+4. **Testing approach?** (Unit tests only or integration tests with real NX)
+5. **Documentation format?** (Markdown, Sphinx, MkDocs)
+
+## Getting Help
+
+When you're ready to start coding:
+
+1. Choose a phase from the options above
+2. Tell me which component you want to build first
+3. I'll create the detailed implementation with working code
+4. We'll test it with your existing .sim files
+5. Iterate and expand
+
+---
+
+**You're all set!** The foundation is ready. Choose your starting point and let's build! 🚀

GITHUB_SETUP.md

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+# GitHub Setup Guide
+
+## Creating the Private Repository
+
+1. **Go to GitHub**: https://github.com/new
+
+2. **Repository Settings**:
+   - **Owner**: Your GitHub username or organization (e.g., `atomaste`)
+   - **Repository name**: `nx-optimaster` (or your preferred name)
+   - **Description**: "Advanced optimization platform for Siemens NX Simcenter with LLM integration"
+   - **Visibility**: ✅ **Private**
+   - **DO NOT** initialize with README, .gitignore, or license (we already have these)
+
+3. **Click "Create repository"**
+
+## Pushing to GitHub
+
+After creating the repository on GitHub, run these commands:
+
+```bash
+cd /c/Users/antoi/Documents/Atomaste/Atomizer
+
+# Add the remote repository
+git remote add origin https://github.com/YOUR-USERNAME/nx-optimaster.git
+
+# OR if using SSH:
+# git remote add origin git@github.com:YOUR-USERNAME/nx-optimaster.git
+
+# Push the initial commit
+git branch -M main
+git push -u origin main
+```
+
+## Verify Push
+
+Visit your repository at: `https://github.com/YOUR-USERNAME/nx-optimaster`
+
+You should see:
+- README.md displayed on the main page
+- All 12 files committed
+- Private repository badge
+
+## Next Steps
+
+### Set Up GitHub Actions (Optional)
+
+Create `.github/workflows/tests.yml` for automated testing:
+
+```yaml
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - run: pip install -r requirements.txt
+      - run: pytest
+```
+
+### Protect Main Branch
+
+Settings → Branches → Add rule:
+- Branch name pattern: `main`
+- ✅ Require pull request reviews before merging
+- ✅ Require status checks to pass
+
+### Add Collaborators
+
+Settings → Collaborators → Add people
+
+## Clone on Another Machine
+
+```bash
+git clone https://github.com/YOUR-USERNAME/nx-optimaster.git
+cd nx-optimaster
+pip install -r requirements.txt
+```
+
+## Useful Git Commands
+
+```bash
+# Check status
+git status
+
+# View commit history
+git log --oneline
+
+# Create a new branch
+git checkout -b feature/new-feature
+
+# Push branch to GitHub
+git push -u origin feature/new-feature
+
+# Pull latest changes
+git pull origin main
+```
+
+---
+
+**Note**: Replace `YOUR-USERNAME` with your actual GitHub username throughout this guide.