cyanheads/atlas-mcp-server

git clone https://github.com/cyanheads/atlas-mcp-server.git && cd atlas-mcp-server
npm install
docker-compose up -d (start Neo4j) and set NEO4J_URI/NEO4J_USER/NEO4J_PASSWORD in .env
npm run build

Usage

• •npm run start:stdio (default transport) or npm run start:http (Streamable HTTP on 127.0.0.1:3010)
• •Add to client config: { "mcpServers": { "atlas-mcp-server-stdio": { "command": "node", "args": ["/full/path/to/atlas-mcp-server/dist/index.js"], "env": { "NEO4J_URI": "bolt://localhost:7687", ... } } } }
• •Backup: npm run db:backup; restore: npm run db:import <path_to_backup_directory>
• •npm run webui opens the experimental browser Web UI

Key features

• ✓3-node system (Projects, Tasks, Knowledge) with dependency management and cross-entity unified search
• ✓Project/task/knowledge CRUD tools with single/bulk modes (atlas_project_*, atlas_task_*, atlas_knowledge_*), atlas_unified_search (full-text, fuzzy, regex) and atlas_deep_research (creates a hierarchical research plan)
• ✓Neo4j graph database with ACID transactions, property-based fuzzy search, and scalable queries
• ✓MCP resources: atlas://projects, atlas://tasks, atlas://knowledge plus resource templates per entity
• ✓JSON-based database backup/restore (projects.json, tasks.json, knowledge.json, relationships.json, full-export.json)

Best for

Agent-managed project/task/knowledge tracking with a graph database for complex, dependency-linked workflows and deep-research plan scaffolding.

Caveats

• ⚠Requires a Neo4j instance — self-hosted via Docker (docker-compose included) or Neo4j AuraDB cloud; v1.5.4 was the last SQLite version, v2.0+ is rewritten for Neo4j
• ⚠atlas_database_clean is destructive — it completely resets the database (requires acknowledgement: true)
• ⚠Restoring from a backup is destructive and overwrites all current Neo4j data
• ⚠HTTP transport production use has not been tested yet (MCP_AUTH_SECRET_KEY note); rate limiting defaults to 100 requests/min/IP