docs

MCP Tools

Connect any MCP server to your agents — GitHub, Slack, filesystem, browser, and more.

Ninetrix uses the Model Context Protocol (MCP) as its tool layer. Agents call a local MCP gateway, which routes requests to connected MCP workers. Workers spawn MCP server subprocesses — any MCP-compatible server works.

Architecture

Agent calls POST /v1/mcp/{workspace_id} on the MCP gateway
MCP Gateway routes the call via WebSocket to the correct worker
MCP Worker forwards it to the appropriate subprocess (npx, uvx, python, docker)
Tool result flows back the same path to the agent

Configure MCP servers

Add servers to ~/.agentfile/mcp-worker.yaml. This file is shared across all your agents:

~/.agentfile/mcp-worker.yaml

servers:
  # Web search
  - name: brave-search
    type: npx
    package: "@modelcontextprotocol/server-brave-search"
    env:
      BRAVE_API_KEY: "${BRAVE_API_KEY}"

  # GitHub
  - name: github
    type: npx
    package: "@modelcontextprotocol/server-github"
    env:
      GITHUB_PERSONAL_ACCESS_TOKEN: "${GITHUB_TOKEN}"

  # Filesystem (scoped to a directory)
  - name: filesystem
    type: npx
    package: "@modelcontextprotocol/server-filesystem"
    args: ["${HOME}/projects"]

  # Slack
  - name: slack
    type: npx
    package: "@modelcontextprotocol/server-slack"
    env:
      SLACK_BOT_TOKEN: "${SLACK_BOT_TOKEN}"

  # Notion
  - name: notion
    type: npx
    package: "@notionhq/notion-mcp-server"
    env:
      NOTION_API_KEY: "${NOTION_API_KEY}"

  # Python-based MCP server
  - name: my-tools
    type: uvx
    package: my-tools-package

  # Custom command
  - name: internal-api
    type: command
    command: python /path/to/my_mcp_server.py

Environment variable interpolation

${VAR} in mcp-worker.yaml is resolved from the worker container's environment at runtime. Credentials never leave your network.

Reference tools in agentfile.yaml

agentfile.yaml

agents:
  my-agent:
    tools:
      - name: web_search
        source: mcp://brave-search        # matches server "name" in mcp-worker.yaml

      - name: github
        source: mcp://github

      - name: files
        source: mcp://filesystem

Tool naming

Tool calls are namespaced as {server_name}__{tool_name} to prevent collisions. For example, a GitHub server named github exposes tools like github__create_issue, github__list_pull_requests, etc.

List available tools

Bash

ninetrix mcp list --file agentfile.yaml   # list tools the agent will receive
ninetrix mcp list                          # list all registered servers

Server types

Type	Runs via	Example
`npx`	`npx -y <package>`	Most MCP servers from npm
`uvx`	`uvx <package>`	Python MCP packages via uv
`python`	`python -m <module>`	Python module
`docker`	`docker run <image>`	Containerized MCP server
`command`	arbitrary shell command	Custom scripts

#Architecture

#Configure MCP servers

#Reference tools in agentfile.yaml

#Tool naming

#List available tools