feat: implement SQLite memory persistence for MCP server operations

[ruvnet]

Summary

This PR implements comprehensive SQLite memory persistence for MCP server operations, replacing the previous JSON-based storage system. All memory operations now persist to a robust SQLite database with enhanced schema and cross-session compatibility.

Key Changes

🗄️ SQLite Memory System

• Enhanced SQLite Schema: 12 specialized tables for comprehensive memory management
• Persistent Storage: .swarm/memory.db with WAL mode for concurrent access
• Cross-Session Persistence: Memory survives across Claude Code sessions
• Namespace Support: Organized memory with hierarchical access patterns

🔧 MCP Server Integration

• EnhancedMemory Class: Extends SqliteMemoryStore with full schema support
• 14 Hook Types: Comprehensive operation tracking and persistence
• Memory Synchronization: Shared storage between CLI and MCP tools
• Error Handling: Robust error recovery and database integrity checks

📁 Project Organization

• Archive Legacy Systems: Moved old memory and infrastructure to archive/
• Clean Root Structure: Organized project layout for better maintainability
• Updated Documentation: README reflects new SQLite-based architecture

🔗 NPM Package Updates

• Include SQLite Files: Updated .npmignore to include memory JS/SQL files
• MCP Server Distribution: Includes MCP server files in npm package
• Version Progression: Published alpha.39, alpha.40, alpha.41 with progressive fixes

Technical Details

Database Schema

• 11 Additional Tables: Beyond basic key-value storage
• Agent Interactions: Track multi-agent coordination patterns
• Training Data: Store neural network training information
• Performance Metrics: Monitor and optimize system performance
• Error Logs: Comprehensive error tracking and analysis

Files Modified

• ✅ README.md - Updated to reflect SQLite memory system
• ✅ .npmignore - Include memory and MCP server files
• ✅ src/mcp/mcp-server.js - Enhanced with SQLite persistence
• ✅ Database files in .swarm/ - New SQLite storage location
• ✅ Legacy systems archived to archive/ directory

Features Implemented

• Memory Persistence: All MCP memory operations persist to SQLite
• Enhanced Schema: 12 specialized tables for comprehensive storage
• Cross-Tool Compatibility: CLI and MCP tools share same database
• Performance Optimization: Efficient SQLite operations with indexing
• Error Recovery: Robust handling of database corruption/issues

Testing Completed

• ✅ Memory Operations: Store, retrieve, list, delete operations
• ✅ Hook Integration: All 14 hook types persist correctly
• ✅ Cross-Session: Memory survives Claude Code restarts
• ✅ NPM Distribution: Package includes all necessary files
• ✅ Schema Validation: Enhanced schema properly applied

Breaking Changes

• Storage Location: Memory moved from JSON files to .swarm/memory.db
• API Compatibility: All existing memory APIs remain compatible
• Migration: Automatic migration from JSON to SQLite (if needed)

Performance Impact

• Improved Reliability: SQLite ACID properties ensure data integrity
• Better Concurrency: WAL mode supports concurrent access
• Reduced Memory Usage: Efficient storage with proper indexing
• Faster Queries: SQL-based searching and filtering

Resolves

• Closes BUG: MCP server memory operations don't persist to disk #198 - MCP server memory operations not persisting to disk

🤖 Generated with Claude Code