atlas-mcp-server

Name: atlas-mcp-server
Author: cyanheads

Issues

A Model Context Protocol (MCP) server for ATLAS, a Neo4j-powered task management system for LLM Agents - implementing a three-tier architecture (Projects, Tasks, Knowledge) to manage complex workflows. Now with Deep Research.

476stars

67forks

TypeScript

Installation

# Add to your Claude Code skills
git clone https://github.com/cyanheads/atlas-mcp-server

Getting Started

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Security ReportIssues

Last scanned: 10/5/2026

{
  "issues": [
    {
      "type": "npm-audit",
      "message": "@modelcontextprotocol/sdk: @modelcontextprotocol/sdk has cross-client data leak via shared server/transport instance reuse",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "ajv: ajv has ReDoS when using `$data` option",
      "severity": "medium"
    },
    {
      "type": "npm-audit",
      "message": "axios: Axios is vulnerable to DoS attack through lack of data size check",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "body-parser: body-parser is vulnerable to denial of service when url encoding is used",
      "severity": "medium"
    },
    {
      "type": "npm-audit",
      "message": "brace-expansion: brace-expansion Regular Expression Denial of Service vulnerability",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "diff: jsdiff has a Denial of Service vulnerability in parsePatch and applyPatch",
      "severity": "low"
    },
    {
      "type": "npm-audit",
      "message": "follow-redirects: follow-redirects leaks Custom Authentication Headers to Cross-Domain Redirect Targets",
      "severity": "medium"
    },
    {
      "type": "npm-audit",
      "message": "form-data: form-data uses unsafe random function in form-data for choosing boundary",
      "severity": "critical"
    },
    {
      "type": "npm-audit",
      "message": "js-yaml: js-yaml has prototype pollution in merge (<<)",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "jws: auth0/node-jws Improperly Verifies HMAC Signature",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "linkify-it: LinkifyIt#match scan loop has quadratic algorithmic complexity",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "markdown-it: markdown-it is has a Regular Expression Denial of Service (ReDoS)",
      "severity": "medium"
    },
    {
      "type": "npm-audit",
      "message": "minimatch: minimatch has a ReDoS via repeated wildcards with non-matching literal in pattern",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "moment: moment vulnerable to Path Traversal via crafted non-string locale name",
      "severity": "medium"
    },
    {
      "type": "npm-audit",
      "message": "nanoid: nanoid: non-secure generators can loop indefinitely with negative size",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "path-to-regexp: path-to-regexp vulnerable to Denial of Service via sequential optional groups",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "postcss: PostCSS has XSS via Unescaped </style> in its CSS Stringify Output",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "qs: qs's arrayLimit bypass in comma parsing allows denial of service",
      "severity": "medium"
    },
    {
      "type": "npm-audit",
      "message": "sanitize-html: sanitize-html has incomplete URI scheme validation in that allows javascript: URIs through action, formaction, data, poster, and background attributes",
      "severity": "medium"
    },
    {
      "type": "npm-audit",
      "message": "validator: validator.js has a URL validation bypass vulnerability in its isURL function",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "ws: ws: Uninitialized memory disclosure",
      "severity": "high"
    },
    {
      "type": "npm-audit",
      "message": "yaml: yaml is vulnerable to Stack Overflow via deeply nested YAML collections",
      "severity": "medium"
    }
  ],
  "status": "FAILED",
  "scannedAt": "2026-10-05T11:12:30.349Z",
  "npmAuditRan": true,
  "pipAuditRan": true,
  "promptInjectionRan": true
}

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README.md

Frequently Asked Questions

What is atlas-mcp-server?

atlas-mcp-server is an open-source ai agents skill for AI coding assistants such as Claude Code, Codex CLI, and ChatGPT, built by cyanheads. A Model Context Protocol (MCP) server for ATLAS, a Neo4j-powered task management system for LLM Agents - implementing a three-tier architecture (Projects, Tasks, Knowledge) to manage complex workflows. Now with Deep Research. It has 476 GitHub stars.

Is atlas-mcp-server safe to use?

atlas-mcp-server failed SkillsLLM's automated security scan, which flagged one or more high-severity issues. Review the Security Report section carefully before using it.

How do I install atlas-mcp-server?

Clone the repository with "git clone https://github.com/cyanheads/atlas-mcp-server" and add it to your Claude Code skills directory (see the Installation section above).

What programming language is atlas-mcp-server written in?

atlas-mcp-server is primarily written in TypeScript. It is open-source under cyanheads on GitHub, so you can review or fork the full source.

Are there alternatives to atlas-mcp-server?

Yes. SkillsLLM lists many other AI Agents skills you can browse and compare side by side. Open the AI Agents category from the badge at the top of this page, or use the Related Skills and comparison links further down to weigh atlas-mcp-server against similar tools.

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Related Skills

ECC

by affaan-m

The agent harness performance optimization system. Skills, instincts, memory, security, and research-first development for Claude Code, Codex, Opencode, Cursor and beyond.

273,221

Pane director

ATLAS: Task Management System

ATLAS (Adaptive Task & Logic Automation System) is a project, knowledge, and task management system for LLM Agents.

Built on a 3-node architecture:

                  +-------------------------------------------+
                  |                PROJECT                    |
                  |-------------------------------------------|
                  | id: string                                |
                  | name: string                              |
                  | description: string                       |
                  | status: string                            |
                  | urls?: Array<{title: string, url: string}>|
                  | completionRequirements: string            |
                  | outputFormat: string                      |
                  | taskType: string                          |
                  | createdAt: string                         |
                  | updatedAt: string                         |
                  +----------------+--------------------------+
                            |                    |
                            |                    |
                            v                    v
+----------------------------------+ +----------------------------------+
|               TASK               | |            KNOWLEDGE             |
|----------------------------------| |----------------------------------|
| id: string                       | | id: string                       |
| projectId: string                | | projectId: string                |
| title: string                    | | text: string                     |
| description: string              | | tags?: string[]                  |
| priority: string                 | | domain: string                   |
| status: string                   | | citations?: string[]             |
| assignedTo?: string              | | createdAt: string                |
| urls?: Array<{title: string,     | |                                  |
|   url: string}>                  | | updatedAt: string                |
| tags?: string[]                  | |                                  |
| completionRequirements: string   | |                                  |
| outputFormat: string             | |                                  |
| taskType: string                 | |                                  |
| createdAt: string                | |                                  |
| updatedAt: string                | |                                  |
+----------------------------------+ +----------------------------------+

Implemented as a Model Context Protocol (MCP) server, ATLAS allows LLM agents to interact with a project management database, enabling them to manage projects, tasks, and knowledge items.

Important Version Note: Version 1.5.4 is the last version that uses SQLite as the database. Version 2.0 and onwards has been completely rewritten to use Neo4j, which requires either:

Self-hosting using Docker (docker-compose included in repository)

Using Neo4j AuraDB cloud service: https://neo4j.com/product/auradb/

Version 2.5.0 introduces a new 3-node system (Projects, Tasks, Knowledge) that replaces the previous structure.

Overview
Features
Installation
Running the Server
Web UI (Experimental)
Configuration
Project Structure
Tools
Resources
Database Backup and Restore
Examples
License

Overview

ATLAS implements the Model Context Protocol (MCP), enabling standardized communication between LLMs and external systems through:

Clients: Claude Desktop, IDEs, and other MCP-compatible clients
Servers: Tools and resources for project, task, and knowledge management
LLM Agents: AI models that leverage the server's management capabilities

System Integration

The Atlas Platform integrates these components into a cohesive system:

Project-Task Relationship: Projects contain tasks that represent actionable steps needed to achieve project goals. Tasks inherit context from their parent project while providing granular tracking of individual work items.
Knowledge Integration: Both projects and tasks can be enriched with knowledge items, providing team members with necessary information and context.
Dependency Management: Both projects and tasks support dependency relationships, allowing for complex workflows with prerequisites and sequential execution requirements.
Unified Search: The platform provides cross-entity search capabilities, allowing users to find relevant projects, tasks, or knowledge based on various criteria.

Features

Feature Area	Key Capabilities
Project Management	- Comprehensive Tracking: Manage project metadata, statuses, and rich content (notes, links, etc.) with built-in support for bulk operations.- Dependency & Relationship Handling: Automatically validate and track inter-project dependencies.
Task Management	- Task Lifecycle Management: Create, track, and update tasks through their entire lifecycle.- Prioritization & Categorization: Assign priority levels and categorize tasks with tags for better organization.- Dependency Tracking: Establish task dependencies to create structured workflows.
Knowledge Management	- Structured Knowledge Repository: Maintain a searchable repository of project-related information.- Domain Categorization: Organize knowledge by domain and tags for easy retrieval.- Citation Support: Track sources and references for knowledge items.
Graph Database Integration	- Native Relationship Management: Leverage Neo4j's ACID-compliant transactions and optimized queries for robust data integrity.- Advanced Search & Scalability: Perform property-based searches with fuzzy matching and wildcards while maintaining high performance.
Unified Search	- Cross-Entity Search: Find relevant projects, tasks, or knowledge based on content, metadata, or relationships.- Flexible Query Options: Support for case-insensitive, fuzzy, and advanced filtering options.

Installation

Clone the repository:

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

Install dependencies:
```
npm install
```
Configure Neo4j: Ensure you have a Neo4j instance running and accessible. You can start one using the provided Docker configuration:
```
docker-compose up -d
```
Update your .env file with the Neo4j connection details (see Configuration).
Build the project:
```
npm run build
```

Running the Server

Most MCP Clients run the server automatically, but you can also run it manually for testing or development purposes using the following commands.

ATLAS MCP Server supports multiple transport mechanisms for communication:

Standard I/O (stdio): This is the default mode and is typically used for direct integration with local MCP clients (like IDE extensions).
```
npm run start:stdio
```
This uses the MCP_TRANSPORT_TYPE=stdio setting.
Streamable HTTP: This mode allows the server to listen for MCP requests over HTTP, suitable for remote clients or web-based integrations.
```
npm run start:http
```
This uses the MCP_TRANSPORT_TYPE=http setting. The server will listen on the host and port defined in your .env file (e.g., MCP_HTTP_HOST and MCP_HTTP_PORT, defaulting to 127.0.0.1:3010). Ensure your firewall allows connections if accessing remotely.

Web UI (Experimental)

A basic Web UI is available for viewing Project, Task, & Knowledge details.

Opening the UI:
- To open the UI directly in your browser, run the following command in your terminal:
```
npm run webui
```
Functionality:
- You can see an example screenshot of the Web UI here.

Configuration

Environment Variables

Environment variables should be set in the client config in your

atlas-mcp-server

Compare with similar skills

Frequently Asked Questions

What is atlas-mcp-server?

Is atlas-mcp-server safe to use?

How do I install atlas-mcp-server?

What programming language is atlas-mcp-server written in?

Are there alternatives to atlas-mcp-server?

Related Skills

ATLAS: Task Management System

Table of Contents

Overview

System Integration

Features

Installation

Running the Server

Web UI (Experimental)

Configuration

Environment Variables