feat: Major update with validators, skills, dashboard, and docs reorganization

- Add validation framework (config, model, results, study validators)
- Add Claude Code skills (create-study, run-optimization, generate-report,
  troubleshoot, analyze-model)
- Add Atomizer Dashboard (React frontend + FastAPI backend)
- Reorganize docs into structured directories (00-09)
- Add neural surrogate modules and training infrastructure
- Add multi-objective optimization support

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

.claude/skills/create-study.md

@@ -1,7 +1,7 @@
 # Create Optimization Study Skill
 
-**Last Updated**: November 24, 2025
-**Version**: 1.0 - Complete Study Scaffolding
+**Last Updated**: November 25, 2025
+**Version**: 1.1 - Complete Study Scaffolding with Validator Integration
 
 You are helping the user create a complete Atomizer optimization study from a natural language description.
 
@@ -18,6 +18,8 @@ Guide the user through an interactive conversation to:
 
 A complete Atomizer study has this structure:
 
+**CRITICAL**: All study files, including README.md and results, MUST be located within the study directory. NEVER create study documentation at the project root.
+
 ```
 studies/{study_name}/
 ├── 1_setup/
@@ -33,7 +35,7 @@ studies/{study_name}/
 │   └── [various analysis files]
 ├── run_optimization.py              # YOU GENERATE THIS
 ├── reset_study.py                   # YOU GENERATE THIS
-├── README.md                        # YOU GENERATE THIS
+├── README.md                        # YOU GENERATE THIS (INSIDE study directory!)
 └── NX_FILE_MODIFICATIONS_REQUIRED.md  # YOU GENERATE THIS (if needed)
 ```
 
@@ -275,6 +277,10 @@ except Exception as e:
 
 ### 5. README.md
 
+**CRITICAL: ALWAYS place README.md INSIDE the study directory at `studies/{study_name}/README.md`**
+
+Never create study documentation at the project root. All study-specific documentation must be centralized within the study directory structure.
+
 Comprehensive documentation including:
 - Engineering scenario and context
 - Problem statement with real-world constraints
@@ -289,6 +295,7 @@ Comprehensive documentation including:
 - Comparison with other studies
 - Technical notes
 
+**Location**: `studies/{study_name}/README.md` (NOT at project root)
 **Template**: Use [studies/drone_gimbal_arm_optimization/README.md](../studies/drone_gimbal_arm_optimization/README.md:1) as reference
 
 ### 6. NX_FILE_MODIFICATIONS_REQUIRED.md (if needed)
@@ -441,6 +448,91 @@ Extractors: extract_solid_stress, extract_displacement
 Multi-Solution: No (static only)
 ```
 
+## Validation Integration
+
+After generating files, always validate the study setup using the validator system:
+
+### Config Validation
+
+```python
+from optimization_engine.validators import validate_config_file
+
+result = validate_config_file("studies/{study_name}/1_setup/optimization_config.json")
+if result.is_valid:
+    print("[OK] Configuration is valid!")
+else:
+    for error in result.errors:
+        print(f"[ERROR] {error}")
+```
+
+### Model Validation
+
+```python
+from optimization_engine.validators import validate_study_model
+
+result = validate_study_model("{study_name}")
+if result.is_valid:
+    print(f"[OK] Model files valid!")
+    print(f"    Part: {result.prt_file.name}")
+    print(f"    Simulation: {result.sim_file.name}")
+else:
+    for error in result.errors:
+        print(f"[ERROR] {error}")
+```
+
+### Complete Study Validation
+
+```python
+from optimization_engine.validators import validate_study
+
+result = validate_study("{study_name}")
+print(result)  # Shows complete health check
+```
+
+### Validation Checklist for Generated Studies
+
+Before declaring a study complete, ensure:
+
+1. **Config Validation Passes**:
+   - All design variables have valid bounds (min < max)
+   - All objectives have proper extraction methods
+   - All constraints have thresholds defined
+   - Protocol matches objective count
+
+2. **Model Files Ready** (user must provide):
+   - Part file (.prt) exists in model directory
+   - Simulation file (.sim) exists
+   - FEM file (.fem) will be auto-generated
+
+3. **Run Script Works**:
+   - Test with `python run_optimization.py --trials 1`
+   - Verify imports resolve correctly
+   - Verify NX solver can be reached
+
+### Automated Pre-Flight Check
+
+Add this to run_optimization.py:
+
+```python
+def preflight_check():
+    """Validate study setup before running."""
+    from optimization_engine.validators import validate_study
+
+    result = validate_study(STUDY_NAME)
+
+    if not result.is_ready_to_run:
+        print("[X] Study validation failed!")
+        print(result)
+        sys.exit(1)
+
+    print("[OK] Pre-flight check passed!")
+    return True
+
+if __name__ == "__main__":
+    preflight_check()
+    # ... rest of optimization
+```
+
 ## Critical Reminders
 
 ### Multi-Objective Return Format