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>

generated_hooks/hook_constraint_yield_constraint.py

@@ -0,0 +1,83 @@
+"""
+Constraint Check Hook
+Auto-generated by Atomizer Phase 2.9
+
+Check if stress is below yield
+
+Constraint: max_stress / yield_strength
+Threshold: 1.0
+"""
+
+import sys
+import json
+from pathlib import Path
+
+
+def check_yield_constraint(max_stress, yield_strength):
+    """
+    Check constraint condition.
+
+    Args:
+        max_stress: float
+        yield_strength: float
+
+    Returns:
+        tuple: (satisfied: bool, value: float, violation: float)
+    """
+    value = max_stress / yield_strength
+    satisfied = value <= 1.0
+    violation = max(0.0, value - 1.0)
+
+    return satisfied, value, violation
+
+
+def main():
+    """Main entry point for hook execution."""
+    if len(sys.argv) < 2:
+        print("Usage: python {} <input_file.json>".format(sys.argv[0]))
+        sys.exit(1)
+
+    input_file = Path(sys.argv[1])
+
+    # Read inputs
+    with open(input_file, 'r') as f:
+        inputs = json.load(f)
+
+    # Extract required inputs
+    max_stress = inputs.get("max_stress")
+    if max_stress is None:
+        print(f"Error: Required input 'max_stress' not found")
+        sys.exit(1)
+    yield_strength = inputs.get("yield_strength")
+    if yield_strength is None:
+        print(f"Error: Required input 'yield_strength' not found")
+        sys.exit(1)
+
+    # Check constraint
+    satisfied, value, violation = check_yield_constraint(max_stress, yield_strength)
+
+    # Write output
+    output_file = input_file.parent / "yield_constraint_check.json"
+    output = {
+        "constraint_name": "yield_constraint",
+        "satisfied": satisfied,
+        "value": value,
+        "threshold": 1.0,
+        "violation": violation,
+        "inputs_used": {"max_stress": max_stress, "yield_strength": yield_strength}
+    }
+
+    with open(output_file, 'w') as f:
+        json.dump(output, f, indent=2)
+
+    status = "SATISFIED" if satisfied else "VIOLATED"
+    print(f"Constraint {status}: {value:.6f} (threshold: 1.0)")
+    if not satisfied:
+        print(f"Violation: {violation:.6f}")
+    print(f"Result saved to: {output_file}")
+
+    return value
+
+
+if __name__ == '__main__':
+    main()