tl;dr: Manage enabled and allowed state for servers/tools in the server configuration.

Servers with many tools impact the usability of the tool picker; requiring repeated grooming of the list. Some servers start to provide command line flags to reduce tools; but as a client we can help here.

Out of the box, every single MCP invocation requires a confirmation now. While MCP servers could eventually provide "risk" signals, this should be a configurable user/team-choice in mcp.json to reduce the amount of confirmations.