Modern harnesses don't do that, MCP is also progressive disclosure now. MCP tool descriptions aren't included anymore, and have to be found via tool_search. I actually find that to be a regression. Sometimes the models will start coding a python script for something that is already available via a pre-compiled MCP tool call.
In Claude Code you can enable / disable MCP servers at will, just use the /mcp command. You can also lock down permissions in claude -p headless mode to individual tools within an MCP server (eg maybe you only want to allow the reading tools, and none of the write-enabled tools for your automated session).