docs: add documentation for mcp excludeTools and includeTools

[Seydulla]

TLDR

This PR clarifies the behavior of includeTools and excludeTools configuration options for MCP servers in the CLI configuration documentation.

Dive Deeper

Changes

• Added includeTools description: Added clarification that it creates a whitelist behavior and that all tools are enabled by default when not specified

• Added excludeTools description: Added note about precedence - excludeTools takes precedence over includeTools

  Testing

• Documentation changes only - no code changes

Linked issues / bugs

Documentation for #2976 changes

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[gemini-code-assist]

Summary of Changes

Hello @Seydulla, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request enhances the security and configurability of Model Context Protocol (MCP) servers by introducing a new option to explicitly exclude certain tools. This allows administrators and users to prevent potentially risky or unwanted tools from being exposed to the model, providing finer-grained control over the available functionalities.

Highlights

• New Configuration Option: Introduced an excludeTools option within the MCPServerConfig to allow users to specify a list of tool names that should not be exposed by a Model Context Protocol (MCP) server.
• Tool Filtering Logic: Implemented logic during the MCP tool discovery process to filter out and prevent the registration of tools listed in the excludeTools configuration for a given server, enhancing security.
• Configuration Merging: Ensured that excludeTools configurations from extensions are properly merged with workspace settings, allowing for a comprehensive list of excluded tools.
• Documentation Updates: Updated both the CLI configuration and extension documentation to reflect the new excludeTools option, including usage examples for clarity.
• Comprehensive Testing: Added new unit tests to validate the correct behavior of the excludeTools functionality, covering scenarios with excluded tools, empty lists, and undefined configurations.

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[gemini-code-assist]

Code Review

This pull request introduces the excludeTools option for MCP server configuration, enhancing security. It includes documentation, unit tests, and addresses issue #3160. To improve robustness, consider validating the excludeTools configuration to prevent potential errors from malformed settings.

[jackwotherspoon]

This feature has already been merged as part of #2976

However, it looks like documentation was missed in the PR.

@Seydulla do you want to update your PR to be a documentation PR for the new excludeTools capability for MCP configs?

If not I will close this PR and I can put up a docs PR myself, but wanted to give you the option first 😄

[Seydulla]

This feature has already been merged as part of #2976

However, it looks like documentation was missed in the PR.

@Seydulla do you want to update your PR to be a documentation PR for the new excludeTools capability for MCP configs?

If not I will close this PR and I can put up a docs PR myself, but wanted to give you the option first 😄

Sure, I will update

[Seydulla]

@jackwotherspoon updated current PR to be a documentation for #2976 changes

[jackwotherspoon]

@Seydulla mind also updating https://github.com/google-gemini/gemini-cli/blob/main/docs/tools/mcp-server.md#optional

Thanks so much for this! 👏 ❤️

[NTaylorMullen]

Thank you for the contribution @Seydulla and reviews @jackwotherspoon and @swissspidy !

Author submitted fixes.