Support for choosing allowed MCP tools

### Feature summary

Finer grained controls over allowing or disallowing MCP tools

### What problem are you trying to solve?

A have a few MCP servers installed but I don't use all of the tools from them. and in some cases I explicitly want to ban these tools. They was a bunch of tokens for me (latest was 90k tokens 🫠)

### Proposed solution

I would like to be able to configure which tools from an MCP are available globally so that I can cut back on the list that is always sent to the agent

### Workflow impact

_No response_

### Installation context

_No response_

### Additional context

_No response_

The issue names no files, tests, or entry points. Start by locating the MCP configuration and tool-registration paths, then trace how the available tool list is assembled for the agent. Done means users can globally allow or deny individual tools and excluded tools no longer appear in the agent’s tool list.

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