MCP Configuration Locations Across AI Development Tools

This document provides a comprehensive guide to where different AI development tools store their Model Context Protocol (MCP) configurations.

Summary of Common Patterns

Most AI development tools store MCP configurations in JSON files with a common structure:

{
  "mcpServers": {
    "server-name": {
      "command": "node",
      "args": ["path/to/server.js"],
      "env": { "KEY": "value" }
    }
  }
}

The most common configuration keys are:

• mcpServers (most common)
• servers (alternative)
• mcp.servers (nested in settings)

Tool-Specific Configuration Locations

1. Claude Desktop

• Location: ~/Library/Application Support/Claude/claude_desktop_config.json (macOS)
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json
• Config Key: mcpServers or mcp_servers

2. Cline AI Coder (VS Code Extension)

• Location: VS Code extension globalStorage
  • macOS: ~/Library/Application Support/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Linux: ~/.config/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
  • Windows: %APPDATA%\Code\User\globalStorage\saoudrizwan.claude-dev\settings\cline_mcp_settings.json
• Config Key: mcpServers or servers

3. VS Code

• Workspace Configuration:
  • .vscode/mcp.json (dedicated MCP file)
  • .vscode/settings.json (in mcp.servers section)
• Global Configuration:
  • macOS: ~/Library/Application Support/Code/User/settings.json
  • Linux: ~/.config/Code/User/settings.json
  • Windows: %APPDATA%\Code\User\settings.json
• Config Key: mcpServers, servers, or mcp.servers (in settings.json)

4. Cursor

• Global: ~/.cursor/mcp.json
• Project: .cursor/mcp.json
• Config Key: mcpServers or servers

5. Windsurf

• Location: ~/.codeium/windsurf/mcp_config.json
• Config Key: mcpServers or servers

6. Continue Dev

• Global: ~/.continue/config.json
• Project: .continue/config.json
• Config Key: mcpServers or contextProviders.mcp

7. Aider

• Location: ~/.aider/config.json or ~/.aider/aider.conf
• Config Key: mcp_servers

8. Generic/Project-Level Configurations

Many tools also check for generic MCP configuration files in the project root:

• mcp.json
• .mcp-config.json
• mcp_config.json
• .mcp-servers.json

Common Configuration Structure

Most tools follow a similar JSON structure:

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "@modelcontextprotocol/server-filesystem",
        "/path/to/allowed/directory"
      ]
    },
    "github": {
      "command": "npx",
      "args": ["@modelcontextprotocol/server-github"],
      "env": {
        "GITHUB_TOKEN": "your-github-token"
      }
    },
    "custom-server": {
      "command": "node",
      "args": ["/path/to/custom/server.js"],
      "cwd": "/path/to/working/directory",
      "env": {
        "CUSTOM_VAR": "value"
      }
    }
  }
}

HTTP Transport Configuration

For remote MCP servers using HTTP/Streamable HTTP transport:

{
  "mcpServers": {
    "remote-api": {
      "transport": "http",
      "url": "https://api.example.com/mcp",
      "headers": {
        "Authorization": "Bearer YOUR_TOKEN"
      },
      "httpOptions": {
        "connectionTimeout": 30000,
        "requestTimeout": 60000,
        "idleTimeout": 120000,
        "keepAliveTimeout": 30000
      },
      "retryConfig": {
        "maxAttempts": 3,
        "initialDelay": 1000,
        "maxDelay": 30000,
        "backoffMultiplier": 2
      },
      "rateLimiting": {
        "requestsPerMinute": 60,
        "maxBurst": 10,
        "useTokenBucket": true
      }
    },
    "oauth-protected-api": {
      "transport": "http",
      "url": "https://api.secure.com/mcp",
      "auth": {
        "type": "oauth2",
        "oauth": {
          "clientId": "your-client-id",
          "clientSecret": "your-client-secret",
          "authorizationUrl": "https://auth.provider.com/authorize",
          "tokenUrl": "https://auth.provider.com/token",
          "redirectUrl": "http://localhost:8080/callback",
          "scope": "mcp:read mcp:write",
          "usePKCE": true
        }
      }
    }
  }
}

HTTP Configuration Options

Option	Type	Description
transport	string	Must be "http" for HTTP transport
url	string	Remote MCP endpoint URL
headers	object	Custom HTTP headers (e.g., Authorization)
httpOptions	object	Connection timeout settings
retryConfig	object	Retry with exponential backoff
rateLimiting	object	Rate limiting configuration
auth	object	OAuth 2.1, Bearer, or API key authentication

See MCP HTTP Transport Guide for complete documentation.

Key Observations

1. Common Pattern: Almost all tools use JSON files with an mcpServers object

2. Location Hierarchy: Tools typically check in this order:

   • Project/workspace specific configs
   • User/global configs
   • Default/fallback configs

3. Platform Differences:

   • macOS: Often uses ~/Library/Application Support/
   • Linux: Typically uses ~/.config/
   • Windows: Usually uses %APPDATA%

4. Extension Storage: VS Code extensions (like Cline) store configs in VS Code's globalStorage

Auto-Discovery Priority

When multiple configurations exist, tools typically prioritize in this order:

1. Workspace/project-specific configurations (highest priority)
2. Tool-specific global configurations
3. Generic project configurations (lowest priority)

Best Practices

1. Project-Specific Servers: Use .vscode/mcp.json or similar for project-specific MCP servers
2. Global Servers: Configure frequently-used servers in your tool's global config
3. Environment Variables: Store sensitive data (API keys) in environment variables
4. Version Control: Commit project-specific configs, exclude global configs with API keys

NeuroLink Auto-Discovery

NeuroLink's MCP auto-discovery system automatically searches all these locations and can discover MCP servers configured in any of these tools. Use the CLI command:

neurolink mcp discover

This will find and list all MCP servers configured across your system, regardless of which tool configured them.