Branch Thinking MCP server for AI agents

Neural Architect is an MCP server tool that enables structured thinking and analysis across multiple AI platforms through branch management, semantic analysis, and cognitive enhancement. It allows AI systems to maintain multiple thought branches, analyze semantic connections, and provide standardized analytics across different AI platforms.

Installation

Platform-Specific Installation

Depending on which platform you want to use Neural Architect with, there are different installation methods:

# For Claude Desktop
{
  "branch-thinking": {
    "command": "node",
    "args": ["/path/to/tools/branch-thinking/dist/index.js"]
  }
}

# For VSCode
ext install mcp-branch-thinking

# For Cursor
cursor plugin install @mcp/branch-thinking

# For Command Line
npm install -g @mcp/branch-thinking-cli

# For Development
npm install @modelcontextprotocol/server-branch-thinking

System Requirements

Component	Requirement	Notes
Node.js	≥18.0.0	Required for MCP protocol
TypeScript	≥5.3.0	For type safety
Memory	≥512MB	Recommended: 1GB
Storage	≥100MB	For caching & analytics
Network	Low latency	<50ms recommended

Usage

Neural Architect can be used on different platforms with specific commands:

# Cursor
/think analyze this problem

# VSCode Copilot
#! branch-thinking: analyze

# Claude
Use branch-thinking to analyze...

# Command Line
na analyze "problem statement"

# Roo
@branch-thinking analyze

# Claude Code
/branch analyze

Basic Commands

The following commands help you manage thought branches:

list                    # Show all thought branches
focus <branchId>        # Switch to specific branch
history [branchId]      # View branch history

Advanced Features

Neural Architect offers powerful analytical capabilities:

semantic-search <query> # Search across thoughts
analyze-branch <id>     # Generate branch analytics
detect-bias <id>        # Check for cognitive biases

Analysis Commands

na semantic-search "query" [--threshold=0.7] [--max=10]
na multi-hop "start" "end" [--depth=3]
na analyze-clusters [--method=dbscan] [--epsilon=0.5]

Monitoring Commands

na analyze branch-name [--metrics=all]
na track node-id [--window=5]
na detect-bias branch-name [--types=all]

MCP Configuration

The Neural Architect MCP server can be configured as follows:

{
  "name": "@modelcontextprotocol/server-branch-thinking",
  "version": "0.2.0",
  "type": "module",
  "bin": {
    "mcp-server-branch-thinking": "dist/index.js"
  },
  "capabilities": {
    "streaming": false,
    "batchProcessing": true,
    "contextAware": true
  }
}

Usage Tips

Direct Invocation
```
Use branch-thinking to analyze...
```

Automatic Triggering Add to Claude's system prompt:

Use branch-thinking when asked to "think step by step" or "analyze thoroughly"

Best Practices
- Start with main branch
- Create sub-branches for alternatives
- Use cross-references for connections
- Monitor bias scores

Supported Platforms

Platform	Status	Integration
Claude	✅	Native support
VSCode Copilot	✅	Via MCP extension
Cursor	✅	Direct integration
Roo	🚧	In development
Command Line	✅	CLI tool
Claude Code	✅	Native support

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "branch-thinking" '{"command":"node","args":["/path/to/tools/branch-thinking/dist/index.js"]}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

{
    "mcpServers": {
        "branch-thinking": {
            "command": "node",
            "args": [
                "/path/to/tools/branch-thinking/dist/index.js"
            ]
        }
    }
}

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: %APPDATA%\Claude\claude_desktop_config.json
Linux: ~/.config/Claude/claude_desktop_config.json

2. Add this to your configuration file:

{
    "mcpServers": {
        "branch-thinking": {
            "command": "node",
            "args": [
                "/path/to/tools/branch-thinking/dist/index.js"
            ]
        }
    }
}

3. Restart Claude Desktop for the changes to take effect