Feat/mcp docker integration

[rapozoantonio]

Description

Major enhancement to the MCP server with new cognitive memory features including entity graphs, embedding support, memory normalization, and quality gates. Adds comprehensive test coverage for retrieval benchmarking, prefrontal routing, and relevance scoring pipelines.

Type

• 🐛 Bug fix
• ✨ New feature
• 🔄 Refactoring
• 📝 Documentation
• ⚡ Performance
• 🚨 Breaking change

Changes

• Add entity graph support (entity-graph.ts) for relationship tracking between memories
• Add embedding module (embedding.ts) for semantic vector operations
• Add memory normalizer (normalizer.ts) for consistent memory formatting
• Add quality gates (quality-gate.ts) to validate memory entries before storage
• Enhanced retrieval with improved prefrontal routing and relevance scoring
• Add comprehensive test suite: benchmarks, MML pipeline, quality gates, retrieval formatting
• Update cognitive amygdala with expanded pattern recognition
• Refactored API client and process manager for better Docker integration

Related Issues

Closes #
Related: #

Testing

# All tests must pass
dotnet test
dotnet build /warnaserror

• Unit tests pass
• Integration tests pass (if applicable)
• Manual testing completed
• New tests added for new features

Breaking Changes

• Memory storage API now includes quality gate validation
• Retrieval response format updated with additional metadata fields
• store-memory tool accepts new optional parameters for embedding and entity linking

Migration Guide (if breaking changes)

1. Update any direct calls to store() to handle potential quality gate rejections
2. Update retrieval consumers to handle new response format with relevanceScore and entityLinks fields
3. Review memory entries that may fail new quality gate validations