atlas-mcp-server vs filesystem

Side-by-side comparison to help you pick between these two MCP servers.

	atlas-mcp-server by cyanheads	filesystem by modelcontextprotocol
Stars	★ 475	★ 85,748
30d uses	—	—
Score	48	77
Official	—	✓
Categories	Knowledge GraphProductivityDeveloper Tools	File SystemDeveloper ToolsProductivity
Language	TypeScript	TypeScript
Last commit	10 mo ago	this month

atlas-mcp-server · Summary

A Neo4j-powered MCP server implementing three-tier project/task/knowledge management for LLM agents with deep research capabilities.

filesystem · Summary

A feature-rich MCP server for filesystem operations with dynamic directory access control.

atlas-mcp-server · Use cases

Managing complex multi-agent workflows with project, task, and knowledge components
Research and development teams tracking project dependencies and knowledge bases
LLM applications that need structured task management with relationship tracking

filesystem · Use cases

Enable AI models to read and write project files during development
Allow Claude or other MCP clients to browse and analyze codebases
Provide secure sandboxed access to specific directories for content generation

atlas-mcp-server · Install

Installation

Clone the repository:

git clone https://github.com/cyanheads/atlas-mcp-server.git
cd atlas-mcp-server

Install dependencies:

npm install

Configure Neo4j (start with Docker):

docker-compose up -d

Update .env with Neo4j connection details.

Build the project:

npm run build

Claude Desktop Configuration

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "atlas": {
      "command": "node",
      "args": ["dist/index.js"],
      "env": {
        "NEO4J_URI": "bolt://localhost:7687",
        "NEO4J_USER": "neo4j",
        "NEO4J_PASSWORD": "yourpassword"
      }
    }
  }
}

filesystem · Install

Installation

Using NPX

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/path/to/allowed/directory"
      ]
    }
  }
}

Using Docker

{
  "mcpServers": {
    "filesystem": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "--mount", "type=bind,src=/path/to/allowed/dir,dst=/projects/allowed/dir",
        "mcp/filesystem",
        "/projects"
      ]
    }
  }
}

VS Code Extension

Click the installation buttons in the README to install directly in VS Code.

Comparison generated from public README + GitHub signals. Last updated automatically.