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The MCP server is configured through environment variables in your .env file: 
# MCP Server Configuration
MCP_ENABLED=true              # Enable/disable MCP server (default: false)
MCP_SERVER_PORT=3001          # Default MCP server port (default: 3001)
RPC_MCP_PORT=3001             # Override port (takes precedence when non-zero)
The node reads RPC_MCP_PORT first and falls back to MCP_SERVER_PORT when RPC_MCP_PORT is 0 or unset. .env.example ships with RPC_MCP_PORT=3001, so both variables resolve to the same port by default.