What concretely do you mean be definitions?

If you mean the configuration of the entry points similar to a .mcp.json for Claude Code, they can exist in any form, but ultimately, that only contains the endpoints of MCP servers (the entry points for discovery for each of the MCP servers).

If you mean the definitions of what tools are part of what MCP server (= the meat of what is involved in tool calling), those definitions are part of the MCP server and are only retrieved at runtime.

> how are the agents aware of them

Same as in Claude Code, the agent (= the control loop for the LLM) contacts the list of MCP endpoints, gathers all of the available tools on each MCP server, and then exposes those tools to the LLM (and handles the interactions between LLM and MCP server).

> There has to be a file somewhere.

Not in any way that's meaningful for an `ls` operation.