refactor: Major project cleanup and reorganization

## Removed Duplicate Directories
- Deleted old `dashboard/` (replaced by atomizer-dashboard)
- Deleted old `mcp_server/` Python tools (moved model_discovery to optimization_engine)
- Deleted `tests/mcp_server/` (obsolete tests)
- Deleted `launch_dashboard.bat` (old launcher)

## Consolidated Code
- Moved `mcp_server/tools/model_discovery.py` to `optimization_engine/model_discovery/`
- Updated import in `optimization_config_builder.py`
- Deleted stub `extract_mass.py` (use extract_mass_from_bdf instead)
- Deleted unused `intelligent_setup.py` and `hybrid_study_creator.py`
- Archived `result_extractors/` to `archive/deprecated/`

## Documentation Cleanup
- Deleted deprecated `docs/06_PROTOCOLS_DETAILED/` (14 files)
- Archived dated dev docs to `docs/08_ARCHIVE/sessions/`
- Archived old plans to `docs/08_ARCHIVE/plans/`
- Updated `docs/protocols/README.md` with SYS_15

## Skills Consolidation
- Archived redundant study creation skills to `.claude/skills/archive/`
- Kept `core/study-creation-core.md` as canonical

## Housekeeping
- Updated `.gitignore` to prevent `nul` and `_dat_run*.dat`

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

archive/deprecated/result_extractors/__init__.py

@@ -0,0 +1,66 @@
+"""
+Pluggable Result Extractor System
+
+Base classes and implementations for extracting metrics from FEA results.
+"""
+
+from abc import ABC, abstractmethod
+from typing import Dict, Any, Optional
+from pathlib import Path
+
+
+class ResultExtractor(ABC):
+    """Base class for all result extractors."""
+
+    @abstractmethod
+    def extract(self, result_files: Dict[str, Path], config: Dict[str, Any]) -> Dict[str, float]:
+        """
+        Extract metrics from FEA results.
+
+        Args:
+            result_files: Dictionary mapping file types to paths (e.g., {'op2': Path(...), 'f06': Path(...)})
+            config: Extractor-specific configuration parameters
+
+        Returns:
+            Dictionary mapping metric names to values
+        """
+        pass
+
+    @property
+    @abstractmethod
+    def required_files(self) -> list[str]:
+        """List of required file types (e.g., ['op2'], ['f06'], etc.)."""
+        pass
+
+    @property
+    def name(self) -> str:
+        """Extractor name for registration."""
+        return self.__class__.__name__.replace("Extractor", "").lower()
+
+
+# Registry of available extractors
+_EXTRACTOR_REGISTRY: Dict[str, type[ResultExtractor]] = {}
+
+
+def register_extractor(extractor_class: type[ResultExtractor]) -> type[ResultExtractor]:
+    """Decorator to register an extractor."""
+    _EXTRACTOR_REGISTRY[extractor_class().name] = extractor_class
+    return extractor_class
+
+
+def get_extractor(name: str) -> Optional[type[ResultExtractor]]:
+    """Get extractor class by name."""
+    return _EXTRACTOR_REGISTRY.get(name)
+
+
+def list_extractors() -> list[str]:
+    """List all registered extractor names."""
+    return list(_EXTRACTOR_REGISTRY.keys())
+
+
+__all__ = [
+    "ResultExtractor",
+    "register_extractor",
+    "get_extractor",
+    "list_extractors",
+]