@danielsimonjr/memory-mcp

v11.1.1

Published

13 days ago

Enhanced MCP memory server with hierarchies, compression, archiving, graph algorithms, semantic search, and 59 advanced tools

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danielsimonjr

mcp model-context-protocol memory knowledge-graph enhanced timestamps tags export graphml analytics semantic-search embeddings

Memory MCP Server

An enhanced fork of the official Model Context Protocol memory server with advanced features for hierarchical nesting, intelligent compression, semantic search, graph algorithms, archiving, advanced search, and multi-format import/export.

Enterprise-grade knowledge graph with 59 tools, hierarchical organization, semantic search with embeddings, graph traversal algorithms, duplicate detection, smart archiving, and sophisticated search capabilities for long-term memory management.

Features

Core Memory Capabilities

Knowledge Graph Storage: Entity-Relation-Observation model for structured memory
Persistent Memory: Information persists across chat sessions with JSONL or SQLite storage
Dual Storage Backends: JSONL (human-readable) or SQLite with better-sqlite3 (3-10x faster, FTS5 search)
Full CRUD Operations: Create, read, update, delete entities and relations
Flexible Search: Text-based, fuzzy, boolean, semantic, and TF-IDF ranked search

Advanced Features

| Category | Tools | Description | |----------|-------|-------------| | Hierarchical Nesting | 9 | Parent-child relationships for organizing tree structures | | Graph Algorithms | 4 | Path finding, connected components, centrality metrics | | Intelligent Search | 3 | Hybrid multi-layer search with query analysis and reflection | | Semantic Search | 3 | Embedding-based similarity search with OpenAI or local models | | Memory Compression | 4 | Intelligent duplicate detection and merging with similarity scoring | | Advanced Search | 7 | TF-IDF ranking, boolean queries, fuzzy matching, auto-select | | Observation Normalization | 1 | Coreference resolution and temporal anchoring | | Tag Management | 11 | Tags, aliases, bulk operations, importance scores | | Saved Searches | 5 | Store and execute frequent queries | | Import/Export | 2 | 7 export formats with brotli compression, 3 import formats | | Graph Analytics | 2 | Statistics, validation, integrity checks |

Comparison with Official Memory Server

| Feature | Official | Enhanced (This Fork) | |---------|----------|----------------------| | Entity/Relation/Observation Management | ✅ | ✅ | | Basic Search | ✅ | ✅ | | Hierarchical Nesting | ❌ | ✅ Parent-child trees | | Graph Algorithms | ❌ | ✅ Path finding, centrality | | Semantic Search | ❌ | ✅ Embedding-based similarity | | Memory Compression | ❌ | ✅ Duplicate detection | | Brotli Compression | ❌ | ✅ Backups, exports, responses | | Smart Archiving | ❌ | ✅ Criteria-based | | Advanced Search | ❌ | ✅ TF-IDF + Boolean + Fuzzy | | SQLite Backend | ❌ | ✅ better-sqlite3 (3-10x faster) | | Full-Text Search | ❌ | ✅ FTS5 with BM25 ranking | | Timestamps | ❌ | ✅ createdAt + lastModified | | Import/Export Formats | ❌ | ✅ 7 export / 3 import | | Input Validation | ❌ | ✅ Zod schemas | | Backup & Restore | ❌ | ✅ Compressed snapshots | | Intelligent Search | ❌ | ✅ Hybrid + Query Analysis + Reflection | | Observation Normalization | ❌ | ✅ Coreference resolution + temporal anchoring | | Total Tools | 11 | 59 | | Code Structure | Monolithic | Modular (77 files) |

Quick Start

1. Install from NPM

npm install -g @danielsimonjr/memory-mcp

Or use with npx (no installation required):

npx @danielsimonjr/memory-mcp

2. Configure Claude Desktop

Add to claude_desktop_config.json:

Using NPM Global Install:

{
  "mcpServers": {
    "memory": {
      "command": "mcp-server-memory"
    }
  }
}

Using NPX:

{
  "mcpServers": {
    "memory": {
      "command": "npx",
      "args": ["-y", "@danielsimonjr/memory-mcp"]
    }
  }
}

3. Restart Claude Desktop

Restart Claude Desktop to load the enhanced memory server.

4. Start Using

Tell Claude:

Please remember that I prefer TypeScript over JavaScript.
Tag this as "preferences" with importance 8.
Create a parent entity called "Development Preferences" and nest this under it.

Installation

Local Build

# Clone repository
git clone https://github.com/danielsimonjr/memory-mcp.git
cd memory-mcp

# Install and build
npm install
npm run build

# Run tests (2800+ tests)
npm test

# Type check
npm run typecheck

Claude Desktop Configuration

Add to ~/Library/Application Support/Claude/claude_desktop_config.json (Mac) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "memory": {
      "command": "node",
      "args": ["<PATH_TO>/memory-mcp/dist/index.js"],
      "env": {
        "MEMORY_FILE_PATH": "<PATH_TO>/memory.jsonl"
      }
    }
  }
}

VS Code

Add to .vscode/mcp.json:

{
  "servers": {
    "memory": {
      "command": "node",
      "args": ["/path/to/memory-mcp/dist/index.js"]
    }
  }
}

Core Concepts

Entities

Primary nodes in the knowledge graph.

interface Entity {
  name: string;           // Unique identifier
  entityType: string;     // Classification
  observations: string[]; // Facts about the entity
  parentId?: string;      // Parent entity name for hierarchical nesting
  tags?: string[];        // Lowercase tags for categorization
  importance?: number;    // 0-10 scale for prioritization
  createdAt?: string;     // ISO 8601 timestamp
  lastModified?: string;  // ISO 8601 timestamp
}

Relations

Directed connections between entities.

interface Relation {
  from: string;           // Source entity name
  to: string;             // Target entity name
  relationType: string;   // Relationship type (active voice)
  createdAt?: string;     // ISO 8601 timestamp
  lastModified?: string;  // ISO 8601 timestamp
}

Observations

Discrete facts about entities. Each observation should be atomic and independently manageable.

API Reference

Complete Tool List (59 Tools)

Entity Operations (4 tools)

| Tool | Description | |------|-------------| | create_entities | Create multiple new entities | | delete_entities | Remove entities and their relations | | read_graph | Read entire knowledge graph | | open_nodes | Retrieve specific nodes by name |

Relation Operations (2 tools)

| Tool | Description | |------|-------------| | create_relations | Create relations between entities | | delete_relations | Remove specific relations |

Observation Management (3 tools)

| Tool | Description | |------|-------------| | add_observations | Add observations to entities | | delete_observations | Remove specific observations | | normalize_observations | Normalize observations (resolve pronouns, anchor dates) |

Search (7 tools)

| Tool | Description | |------|-------------| | search_nodes | Search with filters (tags, importance) | | search_by_date_range | Filter by date range | | search_nodes_ranked | TF-IDF relevance ranking | | boolean_search | Boolean queries (AND/OR/NOT) | | fuzzy_search | Typo-tolerant search | | get_search_suggestions | "Did you mean?" suggestions | | search_auto | Auto-select best search method |

Intelligent Search (3 tools)

| Tool | Description | |------|-------------| | hybrid_search | Multi-layer search combining semantic, lexical, and symbolic signals | | analyze_query | Extract entities, temporal references, and classify query complexity | | smart_search | Reflection-based iterative search until results meet adequacy threshold |

Semantic Search (3 tools)

| Tool | Description | |------|-------------| | semantic_search | Search by semantic similarity using embeddings | | find_similar_entities | Find entities similar to a reference entity | | index_embeddings | Build or rebuild the semantic search index |

Saved Searches (5 tools)

| Tool | Description | |------|-------------| | save_search | Save search query for reuse | | execute_saved_search | Execute a saved search | | list_saved_searches | List all saved searches | | delete_saved_search | Delete a saved search | | update_saved_search | Update saved search parameters |

Tag Management (6 tools)

| Tool | Description | |------|-------------| | add_tags | Add tags to an entity | | remove_tags | Remove tags from an entity | | set_importance | Set entity importance (0-10) | | add_tags_to_multiple_entities | Bulk tag operation | | replace_tag | Replace tag globally | | merge_tags | Merge two tags into one |

Tag Aliases (5 tools)

| Tool | Description | |------|-------------| | add_tag_alias | Create tag synonym | | list_tag_aliases | List all aliases | | remove_tag_alias | Remove an alias | | get_aliases_for_tag | Get aliases for canonical tag | | resolve_tag | Resolve alias to canonical form |

Hierarchical Nesting (9 tools)

| Tool | Description | |------|-------------| | set_entity_parent | Set/remove parent relationship | | get_children | Get immediate children | | get_parent | Get parent entity | | get_ancestors | Get all ancestors (parent chain) | | get_descendants | Get all descendants (recursive) | | get_subtree | Get entity + descendants with relations | | get_root_entities | Get entities with no parent | | get_entity_depth | Get depth in hierarchy | | move_entity | Move entity to new parent |

Graph Algorithms (4 tools)

| Tool | Description | |------|-------------| | find_shortest_path | Shortest path between entities (BFS) | | find_all_paths | All paths with max depth limit | | get_connected_components | Detect isolated subgraphs | | get_centrality | Calculate centrality metrics (degree, betweenness, PageRank) |

Graph Analytics (2 tools)

| Tool | Description | |------|-------------| | get_graph_stats | Comprehensive graph statistics | | validate_graph | Validate graph integrity |

Compression & Archiving (4 tools)

| Tool | Description | |------|-------------| | find_duplicates | Find similar entities by threshold | | merge_entities | Merge multiple entities into one | | compress_graph | Auto compression with dry-run | | archive_entities | Archive by age, importance, or tags |

Import & Export (2 tools)

| Tool | Description | |------|-------------| | export_graph | Export in 7 formats (JSON, CSV, GraphML, GEXF, DOT, Markdown, Mermaid) with compression | | import_graph | Import from JSON/CSV/GraphML with merge strategies |

Configuration

Environment Variables

| Variable | Description | Default | |----------|-------------|---------| | MEMORY_FILE_PATH | Path to storage file | memory.jsonl (current directory) | | MEMORY_STORAGE_TYPE | Storage backend: jsonl or sqlite | jsonl | | MEMORY_EMBEDDING_PROVIDER | Embedding provider: openai, local, or none | none | | MEMORY_OPENAI_API_KEY | OpenAI API key (required if provider is openai) | - | | MEMORY_EMBEDDING_MODEL | Embedding model to use | text-embedding-3-small (OpenAI) / Xenova/all-MiniLM-L6-v2 (local) | | MEMORY_AUTO_INDEX_EMBEDDINGS | Auto-index entities on creation | false |

Storage Backends

| Feature | JSONL (Default) | SQLite (better-sqlite3) | |---------|-----------------|-------------------------| | Format | Human-readable text | Native binary database | | Transactions | Basic | Full ACID with WAL mode | | Full-Text Search | Basic | FTS5 with BM25 ranking | | Performance | Good | 3-10x faster | | Concurrency | Single-threaded | Thread-safe with async-mutex | | Best For | Small graphs, debugging | Large graphs (10k+ entities) |

Using SQLite:

{
  "mcpServers": {
    "memory": {
      "command": "node",
      "args": ["/path/to/memory-mcp/dist/index.js"],
      "env": {
        "MEMORY_STORAGE_TYPE": "sqlite",
        "MEMORY_FILE_PATH": "/path/to/data/memory.db"
      }
    }
  }
}

Storage Files

When you set MEMORY_FILE_PATH, the server automatically creates related files:

/your/data/directory/
├── memory.jsonl                    # Main knowledge graph
├── memory-saved-searches.jsonl     # Saved search queries
├── memory-tag-aliases.jsonl        # Tag synonym mappings
└── .backups/                       # Timestamped backups
    ├── backup_2026-01-08_10-30-00-123.jsonl
    └── backup_2026-01-08_10-30-00-123.jsonl.meta.json

Migration Tool

Convert between JSONL and SQLite formats:

cd tools/migrate-from-jsonl-to-sqlite
npm install && npm run build

# JSONL to SQLite
node dist/migrate-from-jsonl-to-sqlite.js --from memory.jsonl --to memory.db

# SQLite to JSONL
node dist/migrate-from-jsonl-to-sqlite.js --from memory.db --to memory.jsonl

Development

Prerequisites

Node.js 18+
npm 9+
TypeScript 5.6+

Build Commands

npm install           # Install dependencies
npm run build         # Build TypeScript
npm test              # Run tests (2800+ tests)
npm run typecheck     # Strict type checking
npm run watch         # Development watch mode
npm run clean         # Remove dist/ directory
npm run docs:deps     # Generate dependency graph

Architecture

┌─────────────────────────────────────────────────────┐
│  Layer 1: MCP Protocol Layer                        │
│  server/MCPServer.ts + toolDefinitions (59 tools)   │
│  + toolHandlers + responseCompressor                │
└──────────────────────┬──────────────────────────────┘
                       │
┌──────────────────────┴──────────────────────────────┐
│  Layer 2: Managers + Context (Lazy Initialization)  │
│  ManagerContext (aliased as KnowledgeGraphManager)  │
│  • EntityManager   (CRUD + hierarchy + archive)     │
│  • RelationManager (relation CRUD)                  │
│  • SearchManager   (search + compression + stats)   │
│  • IOManager       (import + export + backup)       │
│  • TagManager      (tag aliases)                    │
│  • GraphTraversal  (path finding, centrality)       │
│  • SemanticSearch  (embeddings, similarity)         │
└──────────────────────┬──────────────────────────────┘
                       │
┌──────────────────────┴──────────────────────────────┐
│  Layer 3: Storage Layer                             │
│  core/GraphStorage.ts (JSONL + in-memory cache)     │
│  core/SQLiteStorage.ts (better-sqlite3 + FTS5)      │
│  core/StorageFactory.ts (backend selection)         │
└─────────────────────────────────────────────────────┘

Project Structure

memory-mcp/
├── src/                            # Source (77 TypeScript files)
│   ├── index.ts                    # Entry point
│   ├── core/                       # Core managers (12 files)
│   │   ├── ManagerContext.ts           # Context holder (lazy init)
│   │   ├── EntityManager.ts            # Entity CRUD + hierarchy
│   │   ├── RelationManager.ts          # Relation CRUD
│   │   ├── GraphStorage.ts             # JSONL I/O + caching
│   │   ├── SQLiteStorage.ts            # SQLite with better-sqlite3
│   │   ├── TransactionManager.ts       # ACID transactions
│   │   ├── StorageFactory.ts           # Storage backend factory
│   │   ├── HierarchyManager.ts         # Tree operations
│   │   ├── ObservationManager.ts       # Observation CRUD
│   │   ├── GraphTraversal.ts           # Path finding, centrality
│   │   ├── GraphEventEmitter.ts        # Event system
│   │   └── index.ts
│   ├── server/                     # MCP protocol (4 files)
│   │   ├── MCPServer.ts                # Server setup
│   │   ├── toolDefinitions.ts          # 59 tool schemas
│   │   ├── toolHandlers.ts             # Handler registry
│   │   └── responseCompressor.ts       # Brotli compression
│   ├── search/                     # Search implementations (29 files)
│   │   ├── SearchManager.ts            # Search orchestrator
│   │   ├── BasicSearch.ts              # Text matching
│   │   ├── RankedSearch.ts             # TF-IDF scoring
│   │   ├── BooleanSearch.ts            # AND/OR/NOT logic
│   │   ├── FuzzySearch.ts              # Typo tolerance
│   │   ├── SemanticSearch.ts           # Embedding-based
│   │   ├── EmbeddingService.ts         # Provider abstraction
│   │   ├── VectorStore.ts              # Vector storage
│   │   └── ...                         # + 12 more
│   ├── features/                   # Advanced capabilities (9 files)
│   │   ├── IOManager.ts                # Import/export/backup
│   │   ├── TagManager.ts               # Tag aliases
│   │   ├── AnalyticsManager.ts         # Graph stats
│   │   ├── ArchiveManager.ts           # Entity archival
│   │   ├── CompressionManager.ts       # Duplicate detection
│   │   ├── StreamingExporter.ts        # Large graph exports
│   │   ├── ObservationNormalizer.ts    # Coreference resolution
│   │   ├── KeywordExtractor.ts         # Keyword extraction
│   │   └── index.ts
│   ├── types/                      # TypeScript definitions (2 files)
│   ├── utils/                      # Shared utilities (18 files)
│   └── workers/                    # Worker pool (2 files)
├── tests/                          # Test suite (97 files, 2800+ tests)
│   ├── unit/                       # Unit tests
│   ├── integration/                # Integration tests
│   ├── e2e/                        # End-to-end tests
│   └── performance/                # Benchmarks
├── dist/                           # Compiled output
├── docs/                           # Documentation
│   ├── architecture/               # Architecture docs
│   ├── guides/                     # User guides
│   └── reports/                    # Sprint reports
├── tools/                          # Standalone utilities
│   ├── chunking-for-files/         # File splitting
│   ├── compress-for-context/       # CTON compression
│   ├── create-dependency-graph/    # Dependency analyzer
│   └── migrate-from-jsonl-to-sqlite/
├── CHANGELOG.md                    # Version history
└── README.md                       # This file

Dependencies

Production:

@modelcontextprotocol/sdk: ^1.21.1
better-sqlite3: ^11.7.0
zod: ^4.1.13
async-mutex: ^0.5.0
@danielsimonjr/workerpool: ^10.0.1

Development:

typescript: ^5.6.2
vitest: ^4.0.13
@vitest/coverage-v8: ^4.0.13
@types/better-sqlite3: ^7.6.12

Documentation

Comprehensive documentation in docs/:

Architecture

API.md - Complete API documentation for all 59 tools
ARCHITECTURE.md - Technical architecture and system design
COMPONENTS.md - Component breakdown and responsibilities
OVERVIEW.md - High-level project overview
DEPENDENCY_GRAPH.md - Module dependencies

User Guides

HIERARCHY.md - Parent-child relationships (9 tools)
COMPRESSION.md - Duplicate detection and merging
ARCHIVING.md - Memory lifecycle and archiving
QUERY_LANGUAGE.md - Boolean search syntax

Development

WORKFLOW.md - Development procedures
MIGRATION.md - Version upgrade guide

Contributing

We welcome contributions!

See:

CONTRIBUTING.md - Contribution guidelines
CODE_OF_CONDUCT.md - Community standards

Ways to Help:

Report bugs
Request features
Submit pull requests
Improve documentation
Add tests

Changelog

All notable changes are documented in CHANGELOG.md.

Current version: v10.1.0 - View full changelog

Recent highlights:

v10.1.0: Documentation updates, 5 missing Phase 12 test files, architecture docs refresh
v10.0.0: Phase 12 Performance Optimization - BM25 search, parallel execution, query plan caching, embedding cache, incremental indexing
v9.8.3: SQLite storage support fix, JSON-RPC communication fix

License

MIT License - see LICENSE

Acknowledgments

Original Project

Enhanced fork of Model Context Protocol memory server by Anthropic.

Developer

Daniel Simon Jr.

Major Enhancements

Hierarchical nesting with parent-child relationships
Graph algorithms: path finding, centrality, connected components
Semantic search with embedding-based similarity
Brotli compression for backups, exports, and responses
Memory compression with intelligent duplicate detection
Smart archiving with criteria-based filtering
Advanced search: TF-IDF, boolean, and fuzzy matching
Multi-format import/export with merge strategies
SQLite backend with better-sqlite3 (3-10x faster)
Transaction support with ACID guarantees
Comprehensive test suite (2800+ tests, 97 test files)

Repository: https://github.com/danielsimonjr/memory-mcp NPM: https://www.npmjs.com/package/@danielsimonjr/memory-mcp Issues: https://github.com/danielsimonjr/memory-mcp/issues