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/mesh_update_issue.txt

@@ -0,0 +1,23 @@
+
+The optimization loop is working, but the results show that:
+
+1. ✅ Parameter updates are happening in Bracket.prt
+2. ✅ NX solver is running successfully  
+3. ✅ Results are being extracted from .op2 files
+4. ✅ Optimization loop completes
+5. ❌ BUT: All trials return the SAME stress/displacement values
+
+This indicates that the bracket geometry is NOT actually changing when we update
+the tip_thickness and support_angle parameters. 
+
+The issue is that these expressions exist in Bracket.prt, but they may not be
+linked to any geometric features (sketches, extrudes, etc.) that define the 
+actual bracket shape.
+
+To fix this, the Bracket.prt file needs to be set up so that:
+- The 'tip_thickness' expression controls an actual dimension
+- The 'support_angle' expression controls an actual angle
+- These dimensions are used in sketches/features to define the geometry
+
+Without this, changing the expressions has no effect on the mesh or the analysis results.
+