feat: Add LLM-native development roadmap and reorganize documentation

- Add DEVELOPMENT_ROADMAP.md with 7-phase plan for LLM-driven optimization
  - Phase 1: Plugin system with lifecycle hooks
  - Phase 2: Natural language configuration interface
  - Phase 3: Dynamic code generation for custom objectives
  - Phase 4: Intelligent analysis and decision support
  - Phase 5: Automated HTML/PDF reporting
  - Phase 6: NX MCP server integration
  - Phase 7: Self-improving feature registry

- Update README.md to reflect LLM-native philosophy
  - Emphasize natural language workflows
  - Link to development roadmap
  - Update architecture diagrams
  - Add future capability examples

- Reorganize documentation structure
  - Move old dev docs to docs/archive/
  - Clean up root directory
  - Preserve all working optimization engine code

This sets the foundation for transforming Atomizer into an AI-powered
engineering assistant that can autonomously configure optimizations,
generate custom analysis code, and provide intelligent recommendations.

docs/archive/GITHUB_SETUP.md

@@ -0,0 +1,102 @@
+# GitHub Setup Guide
+
+## Creating the Private Repository
+
+1. **Go to GitHub**: https://github.com/new
+
+2. **Repository Settings**:
+   - **Owner**: `Anto01`
+   - **Repository name**: `Atomizer`
+   - **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/Anto01/Atomizer.git
+
+# OR if using SSH:
+# git remote add origin git@github.com:Anto01/Atomizer.git
+
+# Push the initial commit
+git branch -M main
+git push -u origin main
+```
+
+## Verify Push
+
+Visit your repository at: `https://github.com/Anto01/Atomizer`
+
+You should see:
+- README.md displayed on the main page
+- All 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/Anto01/Atomizer.git
+cd Atomizer
+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
+```