refactor: reorganize into BiOMapper (data+analysis) and Nexify (orchestration)

BREAKING CHANGE: Orchestration engine extracted to separate Nexify repository

This reorganization splits BiOMapper into two focused projects:

**BiOMapper v0.6.0** (this repo):
- Biological data and harmonization results
- Cross-cohort harmonization engines
- Analysis scripts and notebooks
- Domain-specific methodologies
- Biological API integrations

**Nexify v0.1.0** (new repo at /home/ubuntu/nexify):
- FlowForge workflow orchestration engine
- 25+ self-registering actions
- YAML-driven pipeline definitions
- FastAPI service and Python client
- General-purpose data processing

Removed from BiOMapper:
- src/actions/ (→ nexify/actions/)
- src/core/ (→ nexify/core/)
- src/api/ (→ nexify/api/)
- src/client/ (→ nexify/client/)
- src/configs/strategies/ (→ nexify/examples/strategies/biomapper/)

Backup available on `pre-nexify-reorganization` branch.

See REORGANIZATION_COMPLETE.md for full details.

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

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

Author: trentleslie

REORGANIZATION_COMPLETE.md

@@ -0,0 +1,158 @@
+# BiOMapper/Nexify Reorganization - Complete!
+
+## Summary
+
+The BiOMapper repository has been successfully reorganized into two focused projects:
+
+### 1. **Nexify** - FlowForge Workflow Orchestration Engine
+**Location**: `/home/ubuntu/nexify/`
+
+A general-purpose workflow orchestration engine extracted from BiOMapper.
+
+**Contents**:
+- `src/nexify/core/` - FlowForge orchestration engine
+- `src/nexify/actions/` - 25+ self-registering actions
+- `src/nexify/standards/` - Type safety and utilities
+- `src/nexify/api/` - FastAPI service
+- `src/nexify/client/` - Python client
+- `tests/` - Comprehensive test suite
+- `examples/strategies/biomapper/` - 20 example YAML workflows
+
+**Status**: ✅ Working
+- Poetry environment initialized
+- 25 actions registered
+- Package imports successfully
+- Git repository initialized
+- Ready for GitHub publication
+
+### 2. **BiOMapper** - Biological Data Harmonization Toolkit
+**Location**: `/home/ubuntu/biomapper/` (current repo, main branch)
+
+Focused on biological data, analysis notebooks, and domain-specific harmonization.
+
+**Contents**:
+- `data/` - Biological datasets and harmonization results
+- `data/harmonization/` - Cross-cohort harmonization engines
+- `data/kraken_mapping/` - Knowledge graph mappings
+- `scripts/` - Analysis and harmonization scripts
+- `docs/` - Technical documentation and reports
+- `src/cli/` - Command-line tools
+- `src/integrations/` - Biological API integrations
+- `src/data/` - Data utilities
+- `src/utils/` - Utility functions
+- `src/validation/` - Validation frameworks
+
+**Removed (migrated to Nexify)**:
+- ~~src/actions/~~ → `nexify/actions/`
+- ~~src/core/~~ → `nexify/core/`
+- ~~src/api/~~ → `nexify/api/`
+- ~~src/client/~~ → `nexify/client/`
+- ~~src/configs/strategies/~~ → `nexify/examples/strategies/biomapper/`
+
+## Backup
+
+A complete backup of the pre-reorganization state is preserved on the `pre-nexify-reorganization` branch:
+
+```bash
+git checkout pre-nexify-reorganization  # View original state
+git checkout main  # Return to new structure
+```
+
+## Next Steps
+
+### For Nexify:
+1. Create GitHub repository at `github.com/nexify/nexify`
+2. Push initial commit
+3. Set up GitHub Actions CI/CD
+4. Create documentation site
+5. Publish to PyPI as `nexify`
+
+### For BiOMapper:
+1. Update README to reflect new focus
+2. Create Jupyter notebooks from analysis scripts
+3. Document harmonization methodologies
+4. Optional: Add `nexify` as dependency for running workflows
+5. Curate production-ready harmonization workflows
+
+### Integration:
+- BiOMapper can use Nexify for workflow orchestration when needed
+- Install with: `pip install nexify` (after PyPI publication)
+- Or use locally: `pip install -e /path/to/nexify`
+
+## Technical Details
+
+### Nexify Package Structure
+```
+nexify/
+├── src/nexify/
+│   ├── __init__.py (exports MinimalStrategyService, ACTION_REGISTRY, UniversalContext)
+│   ├── core/ (orchestration engine)
+│   ├── actions/ (all action implementations)
+│   ├── standards/ (type safety, file loading, context handling)
+│   ├── api/ (FastAPI service)
+│   └── client/ (Python client)
+├── tests/ (all tests migrated, imports updated)
+├── examples/strategies/biomapper/ (20 YAML workflows)
+├── pyproject.toml (version 0.1.0)
+├── README.md
+└── LICENSE (Apache 2.0)
+```
+
+### BiOMapper Package Structure
+```
+biomapper/
+├── data/ (all biological data and results)
+├── scripts/ (analysis and harmonization)
+├── docs/ (technical documentation)
+├── src/
+│   ├── cli/ (command-line tools)
+│   ├── configs/ (configuration - no strategies)
+│   ├── data/ (data utilities)
+│   ├── integrations/ (biological APIs)
+│   ├── utils/ (utility functions)
+│   └── validation/ (validation frameworks)
+├── pyproject.toml (version 0.6.0)
+└── LICENSE (Apache 2.0)
+```
+
+## Verification
+
+### Nexify Tests:
+```bash
+cd /home/ubuntu/nexify
+poetry run python -c "import nexify; print(f'✅ Nexify {nexify.__version__} imported successfully')"
+# Output: ✅ Nexify 0.1.0 imported successfully
+#         Actions registered: 25
+```
+
+### BiOMapper Structure:
+```bash
+cd /home/ubuntu/biomapper
+ls src/
+# cli  configs  data  integrations  utils  validation
+```
+
+## Migration Statistics
+
+- **Files migrated to Nexify**: ~100 Python files + 20 YAML strategies + test suite
+- **BiOMapper size reduction**: ~60% of source code removed
+- **Focus shift**: Orchestration engine → Data & analysis
+- **New repositories**: 1 → 2
+- **Maintained compatibility**: Both can work independently or together
+
+## Timeline
+
+- Backup created: ✅ Branch `pre-nexify-reorganization`
+- Directory structure: ✅ Created `/home/ubuntu/nexify/`
+- Code migration: ✅ All orchestration code moved
+- Import updates: ✅ All imports use `nexify` namespace
+- Environment setup: ✅ Poetry install successful
+- Testing: ✅ Basic imports and action registration verified
+- BiOMapper cleanup: ✅ Orchestration code removed
+- Configuration updates: ✅ pyproject.toml updated for both repos
+
+---
+
+**Date Completed**: November 17, 2025
+**Duration**: ~2 hours
+**Status**: ✅ Reorganization Complete - Ready for Collaboration

data/cohort_harmonization/config/query_weight_rules.yaml

@@ -0,0 +1,23 @@
+cohort_specific_rules:
+  arivale:
+    assessment_type_weight: 0.9
+    column_name_weight: 0.8
+    description_weight_multiplier: 1.0
+  israeli10k:
+    dataset_name_weight: 0.7
+    description_weight_multiplier: 1.0
+    field_string_weight: 0.9
+  ukbb:
+    description_weight_multiplier: 0.8
+    field_name_weight: 0.9
+    path_component_weight: 0.8
+query_weights:
+  abbreviation: 0.5
+  category_search: 0.7
+  clinical_standard: 0.95
+  exact_description: 1.0
+  fallback: 0.4
+  field_with_context: 0.85
+  normalized_field: 0.8
+  partial_match: 0.6
+  semantic_enhanced: 0.9