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>

optimization_engine/model_discovery/__init__.py

@@ -0,0 +1,19 @@
+"""
+Model Discovery Module
+
+Tools for parsing and analyzing Siemens NX FEA model files:
+- SimFileParser: Parse .sim files (both XML and binary)
+- discover_fea_model: Main function to analyze model capabilities
+"""
+
+from .model_discovery import (
+    SimFileParser,
+    discover_fea_model,
+    format_discovery_result_for_llm,
+)
+
+__all__ = [
+    "SimFileParser",
+    "discover_fea_model",
+    "format_discovery_result_for_llm",
+]