ATLAS Task Management System for Claude Code: Setup & Config

What you can do with ATLAS Task Management System in Claude Code

Graph-backed project planning that keeps agent tasks, dependencies, and supporting knowledge connected.

• Keep cited knowledge connected to project work.
• Search across projects, tasks, and knowledge.
• Create or update projects in bulk.

Before you start: ATLAS Task Management System in Claude Code

• Node.js and npm
• Cloned atlas-mcp-server repository with npm install completed
• Build generated with npm run build
• Reachable Neo4j instance, self-hosted or AuraDB

Replace the absolute entrypoint path after building. The README also provides npm run start:stdio and npm run start:http. HTTP defaults to 127.0.0.1:3010 with a documented /mcp endpoint. Production use is explicitly untested. Only project tool names are visible in the supplied excerpt.

ATLAS Task Management System Claude Code configuration

1. Choose Claude Code configuration scope

   For ATLAS Task Management System, open Project scope: .mcp.json at the repository root. Project JSON: merge into mcpServers; user scope: use the CLI.

2. Add ATLAS Task Management System to Claude Code

   Use the atlas-mcp-server-cyanheads entry below in mcpServers. Keep ATLAS Task Management System's documented stdio connection fields and your other Claude Code entries.

3. Check ATLAS Task Management System in Claude Code

   ATLAS Task Management System: Inspect claude mcp list and /mcp status.

{
  "mcpServers": {
    "atlas-mcp-server-cyanheads": {
      "type": "stdio",
      "command": "node",
      "args": [
        "/full/path/to/atlas-mcp-server/dist/index.js"
      ],
      "env": {
        "NEO4J_URI": "<Neo4j connection URI>",
        "NEO4J_USER": "<Neo4j username>",
        "NEO4J_PASSWORD": "<Neo4j password>",
        "MCP_LOG_LEVEL": "<Optional logging level>",
        "MCP_TRANSPORT_TYPE": "<stdio for this local client configuration>"
      }
    }
  }
}

claude mcp add-json --scope project 'atlas-mcp-server-cyanheads' '{"type":"stdio","command":"node","args":["/full/path/to/atlas-mcp-server/dist/index.js"],"env":{"NEO4J_URI":"<Neo4j connection URI>","NEO4J_USER":"<Neo4j username>","NEO4J_PASSWORD":"<Neo4j password>","MCP_LOG_LEVEL":"<Optional logging level>","MCP_TRANSPORT_TYPE":"<stdio for this local client configuration>"}}'

ATLAS Task Management System tools available to Claude Code

ATLAS Task Management System's stored tool list documents 4 tools; compare it with Claude Code's connected tool list, because the stored list is not a live check.

atlas_project_create

For ATLAS Task Management System's atlas_project_create, review the permission request and arguments in Claude Code before approval.

Create one project or a batch with metadata and dependencies.

atlas_project_list

For ATLAS Task Management System's atlas_project_list, review the permission request and arguments in Claude Code before approval.

atlas_project_update

For ATLAS Task Management System's atlas_project_update, review the permission request and arguments in Claude Code before approval.

atlas_project_delete

For ATLAS Task Management System's atlas_project_delete, review the permission request and arguments in Claude Code before approval.

Delete a project or a batch of projects.

ATLAS Task Management System: full stored tool descriptions

Troubleshooting ATLAS Task Management System in Claude Code

• If ATLAS Task Management System fails to start, check node (Node.js), the working directory, and Claude Code's selected scope; inspect claude mcp list and /mcp.
• ATLAS Task Management System: check MCP_LOG_LEVEL, MCP_TRANSPORT_TYPE, NEO4J_PASSWORD, NEO4J_URI, NEO4J_USER; keep credentials out of shared .mcp.json.
• ATLAS Task Management System uses stdio here: Claude Code must keep the configured process running; protocol output belongs on stdout and diagnostics on stderr.
• Known limitation: Current versions require a Neo4j deployment.
• Known limitation: The basic web interface is experimental.
• Known limitation: The README says production environment use has not been tested.
• General Claude Code troubleshooting lives in the /clients/claude-code guide.

Frequently asked questions