fix: Comprehensive MCP server fixes and configuration consolidation
## Critical Fixes
### 🔧 FalkorDB Support Implementation
- Fixed incomplete FalkorDB support in `factories.py:276`
- Replaced `NotImplementedError` with proper configuration mapping
- FalkorDB now returns valid config dict with uri, password, database fields
### ⚙️ Configuration System Consolidation
- **REMOVED dual configuration systems** - eliminated config inconsistency
- Deleted obsolete files: `config/manager.py`, `config/server_config.py`
- Deleted unused individual configs: `llm_config.py`, `embedder_config.py`, `neo4j_config.py`
- **Unified all configuration** through `config/schema.py`
- Updated imports: `MCPConfig` → `ServerConfig` from schema
- Added missing fields (`use_custom_entities`, `destroy_graph`) to main config
### 🔄 Environment Variable Handling
- **Eliminated duplicate environment variable patterns** across modules
- Consolidated all env handling into single schema-based system
- Removed redundant `from_env()` methods in individual config classes
- All environment variables now handled through pydantic-settings in schema.py
### 🔒 Security Improvements - GitHub Actions
- **Added proper permissions** to both workflow files:
- `contents: read` - Minimal read access to repository
- `id-token: write` - Secure token handling for OIDC
- Follows security best practices for CI/CD workflows
- Prevents overprivileged workflow execution
### 🧪 Test Infrastructure Updates
- Updated validation test file list for new structure
- Fixed test execution path issues with uv detection
- Improved error handling in startup tests
- All syntax validation now passes (8/8 files)
## Verification
✅ **All systems tested and working**:
- Configuration loading and CLI overrides functional
- Import structure validated across all modules
- Main.py wrapper maintains backwards compatibility
- FalkorDB configuration no longer raises NotImplementedError
- GitHub Actions have secure permissions
- No duplicate environment variable handling
## Benefits
- **Simplified Architecture**: Single source of truth for configuration
- **Enhanced Security**: Proper workflow permissions implemented
- **Complete FalkorDB Support**: No more unimplemented features
- **Maintainable Codebase**: Eliminated configuration duplication
- **Secure CI/CD**: Minimal required permissions only
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
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