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.

.claude/settings.local.json

@@ -2,7 +2,16 @@
   "permissions": {
     "allow": [
       "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" -c:*)",
-      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" examples/test_journal_optimization.py)"
+      "Bash(\"c:/Users/antoi/anaconda3/envs/test_env/python.exe\" examples/test_journal_optimization.py)",
+      "Bash(while true)",
+      "Bash(do sleep 30)",
+      "Bash(if pgrep -f \"test_journal_optimization.py\")",
+      "Bash(/dev/null)",
+      "Bash(then echo \"Still running...\")",
+      "Bash(else echo \"Completed!\")",
+      "Bash(break)",
+      "Bash(fi)",
+      "Bash(done)"
     ],
     "deny": [],
     "ask": []