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/TESTING_STRESS_FIX.md

@@ -0,0 +1,87 @@
+# Testing the Stress Extraction Fix
+
+## Issue Fixed
+Previously, stress extraction was returning **0.0 MPa** instead of the expected **~122.91 MPa**.
+
+**Root Cause**: For solid elements (CHEXA, CTETRA, CPENTA), von Mises stress is at **index 9**, not the last column.
+
+**Fix Applied**: Modified [op2_extractor_example.py](optimization_engine/result_extractors/op2_extractor_example.py#L106-L109) to check element type and use correct index.
+
+## How to Test
+
+### 1. Activate your test environment
+```bash
+conda activate test_env
+```
+
+### 2. Run the verification script
+```bash
+python examples/test_stress_fix.py
+```
+
+### Expected Output
+```
+============================================================
+STRESS EXTRACTION FIX VERIFICATION
+============================================================
+
+--- Displacement (baseline test) ---
+Max displacement: 0.315xxx mm
+Node ID: xxx
+OK Displacement extractor working
+
+--- Stress (FIXED - should show ~122.91 MPa) ---
+Max von Mises: 122.91 MPa
+Element ID: 79
+Element type: chexa
+
+SUCCESS! Stress extraction fixed!
+Expected: ~122.91 MPa
+Got:      122.91 MPa
+============================================================
+```
+
+## Alternative: Test All Extractors
+```bash
+python optimization_engine/result_extractors/extractors.py examples/bracket/bracket_sim1-solution_1.op2
+```
+
+## If Successful, Commit the Fix
+```bash
+git add optimization_engine/result_extractors/op2_extractor_example.py
+git commit -m "fix: Correct von Mises stress extraction for solid elements (CHEXA)
+
+- Use index 9 for solid elements (CHEXA, CTETRA, CPENTA)
+- Keep last column for shell elements (CQUAD4, CTRIA3)
+- Fixes stress extraction returning 0.0 instead of actual values (122.91 MPa)"
+
+git push origin main
+```
+
+## Technical Details
+
+### pyNastran OP2 Data Structure for Solid Elements
+- Shape: `[itime, nnodes, 10]`
+- The 10 values are:
+  ```
+  [oxx, oyy, ozz, txy, tyz, txz, o1, o2, o3, von_mises]
+   0    1    2    3    4    5    6   7   8   9
+  ```
+- **Von Mises is at index 9**
+
+### Code Change
+```python
+# BEFORE (WRONG):
+stresses = stress_data.data[0, :, -1]  # Last column - WRONG for CHEXA!
+
+# AFTER (CORRECT):
+if table_name in ['chexa_stress', 'ctetra_stress', 'cpenta_stress']:
+    # Solid elements: von Mises at index 9
+    stresses = stress_data.data[0, :, 9]
+else:
+    # Shell elements: von Mises at last column
+    stresses = stress_data.data[0, :, -1]
+```
+
+## Files Modified
+- [optimization_engine/result_extractors/op2_extractor_example.py](optimization_engine/result_extractors/op2_extractor_example.py) - Lines 103-112