feat: Complete Phase 3 - pyNastran Documentation Integration

Phase 3 implements automated OP2 extraction code generation using
pyNastran documentation research. This completes the zero-manual-coding
pipeline for FEA optimization workflows.

Key Features:
- PyNastranResearchAgent for automated OP2 code generation
- Documentation research via WebFetch integration
- 3 core extraction patterns (displacement, stress, force)
- Knowledge base architecture for learned patterns
- Successfully tested on real OP2 files

Phase 2.9 Integration:
- Updated HookGenerator with lifecycle hook generation
- Added POST_CALCULATION hook point to hooks.py
- Created post_calculation/ plugin directory
- Generated hooks integrate seamlessly with HookManager

New Files:
- optimization_engine/pynastran_research_agent.py (600+ lines)
- optimization_engine/hook_generator.py (800+ lines)
- optimization_engine/inline_code_generator.py
- optimization_engine/plugins/post_calculation/
- tests/test_lifecycle_hook_integration.py
- docs/SESSION_SUMMARY_PHASE_3.md
- docs/SESSION_SUMMARY_PHASE_2_9.md
- docs/SESSION_SUMMARY_PHASE_2_8.md
- docs/HOOK_ARCHITECTURE.md

Modified Files:
- README.md - Added Phase 3 completion status
- optimization_engine/plugins/hooks.py - Added POST_CALCULATION hook

Test Results:
- Phase 3 research agent: PASSED
- Real OP2 extraction: PASSED (max_disp=0.362mm)
- Lifecycle hook integration: PASSED

Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>

README.md

@@ -175,18 +175,25 @@ Atomizer/
 │   ├── runner.py              # Main optimization runner
 │   ├── nx_solver.py           # NX journal execution
 │   ├── nx_updater.py          # NX model parameter updates
+│   ├── pynastran_research_agent.py  # Phase 3: Auto OP2 code gen ✅
+│   ├── hook_generator.py      # Phase 2.9: Auto hook generation ✅
 │   ├── result_extractors/     # OP2/F06 parsers
 │   │   └── extractors.py      # Stress, displacement extractors
 │   └── plugins/               # Plugin system (Phase 1 ✅)
 │       ├── hook_manager.py    # Hook registration & execution
+│       ├── hooks.py           # HookPoint enum, Hook dataclass
 │       ├── pre_solve/         # Pre-solve lifecycle hooks
 │       │   ├── detailed_logger.py
 │       │   └── optimization_logger.py
 │       ├── post_solve/        # Post-solve lifecycle hooks
 │       │   └── log_solve_complete.py
-│       └── post_extraction/   # Post-extraction lifecycle hooks
-│           ├── log_results.py
-│           └── optimization_logger_results.py
+│       ├── post_extraction/   # Post-extraction lifecycle hooks
+│       │   ├── log_results.py
+│       │   └── optimization_logger_results.py
+│       └── post_calculation/  # Post-calculation hooks (Phase 2.9 ✅)
+│           ├── weighted_objective_test.py
+│           ├── safety_factor_hook.py
+│           └── min_to_avg_ratio_hook.py
 ├── dashboard/                  # Web UI
 │   ├── api/                   # Flask backend
 │   ├── frontend/              # HTML/CSS/JS
@@ -309,11 +316,31 @@ User: "Why did trial #34 perform best?"
   - Understands engineering context (PCOMP, CBAR, element forces, etc.)
   - 95%+ expected accuracy with full nuance detection
 
+- [x] **Phase 2.8**: Inline Code Generation ✅
+  - Auto-generates Python code for simple math operations
+  - Handles avg/min/max, normalization, percentage calculations
+  - Direct integration with Phase 2.7 LLM output
+  - Zero manual coding for trivial operations
+
+- [x] **Phase 2.9**: Post-Processing Hook Generation ✅
+  - Auto-generates standalone Python middleware scripts
+  - Integrated with Phase 1 lifecycle hook system
+  - Handles weighted objectives, custom formulas, constraints, comparisons
+  - Complete JSON-based I/O for optimization loops
+  - Zero manual scripting for post-processing operations
+
+- [x] **Phase 3**: pyNastran Documentation Integration ✅
+  - Automated OP2 extraction code generation
+  - Documentation research via WebFetch
+  - 3 core extraction patterns (displacement, stress, force)
+  - Knowledge base for learned patterns
+  - Successfully tested on real OP2 files
+  - Zero manual coding for result extraction!
+
 ### Next Priorities
 
-- [ ] **Phase 2.8**: Inline Code Generation - Auto-generate simple math operations
-- [ ] **Phase 2.9**: Post-Processing Hook Generation - Middleware script generation
-- [ ] **Phase 3**: MCP Integration - Automated research from NX/pyNastran docs
+- [ ] **Phase 3.1**: Integration - Connect Phase 3 to Phase 2.7 LLM workflow
+- [ ] **Phase 3.5**: NXOpen introspection & pattern curation
 - [ ] **Phase 4**: Code generation for complex FEA features
 - [ ] **Phase 5**: Analysis & decision support
 - [ ] **Phase 6**: Automated reporting