fix(core): merge user settings with extension-provided MCP servers

[abhipatel12]

Summary

Fixes a bug where user-defined MCP server settings (like excludeTools) in settings.json were ignored for MCP servers provided by extensions.

Details

When an extension contributes an MCP server, the McpClientManager was previously using the extension's configuration as-is. This PR modifies startExtension to merge the extension's configuration with any matching local user overrides.

It also updates maybeDiscoverMcpServer to allow extensions to "enrich" existing server configurations that were initially registered without an extension ID (which is the case for user-provided overrides).

Related Issues

Fixes the reported issue where excludeTools for the google-workspace extension (and others) were not being respected.

How to Validate

1. Install google-workspace extension.
2. In settings.json, add:

   "mcpServers": {
     "google-workspace": {
       "excludeTools": ["gmail.send"]
     }
   }

3. Run /mcp list.
4. Verify mcp_google-workspace_gmail.send is NOT in the list.

Pre-Merge Checklist

• Updated relevant documentation and README (if needed)
• Added/updated tests (if needed)
• Noted breaking changes (if any)
• Validated on required platforms/methods:
  • MacOS
    • npm run

[gemini-code-assist]

Summary of Changes

Hello, 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 resolves a critical bug where user-defined settings for MCP servers, such as excludeTools, were being overlooked when those servers were introduced by extensions. The changes ensure that user configurations in settings.json are now correctly merged with and take precedence over extension-provided server configurations, allowing for proper customization and control over tool behavior.

Highlights

• Configuration Merging: Implemented merging of user-defined MCP server settings with configurations provided by extensions.
• Extension Start Logic: Updated startExtension to apply local user overrides to extension-contributed MCP server configurations.
• Server Discovery Enhancement: Enhanced maybeDiscoverMcpServer to allow extensions to enrich existing server configurations, particularly those originating from user settings.

Changelog

• packages/core/src/tools/mcp-client-manager.test.ts
  • Renamed a test case to accurately reflect the new merging behavior.
  • Added assertions to verify that user settings are preserved and merged correctly when an extension registers a server that already has a user configuration.
• packages/core/src/tools/mcp-client-manager.ts
  • Modified the startExtension method to retrieve local user MCP server configurations and merge them with extension-provided configurations before discovering the server.
  • Adjusted the maybeDiscoverMcpServer method's logic to prevent an extension from overwriting an existing server configuration if both the existing and new configurations are associated with different extensions.

Activity

• No human activity has been recorded on this pull request yet.

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[gemini-code-assist]

Code Review

This pull request aims to fix a bug where user-defined MCP server settings were being ignored for servers provided by extensions. While no high or critical security vulnerabilities were directly introduced by these changes, the current implementation uses a shallow merge for configuration, which could lead to array properties like excludeTools being replaced instead of combined. This might cause unintended behavior, such as overriding security-related tool exclusions. It is recommended to address this shallow merge issue and add a test case to cover the array-merging logic.

[github-actions]

Size Change: +1.45 kB (+0.01%)

Total Size: 26.1 MB

Filename	Size	Change
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./bundle/oauth2-provider-6MFV3AEM.js	0 B	-9.19 kB (removed)	🏆
./bundle/chunk-KTF47ICA.js	13.4 MB	+13.4 MB (new file)	🆕
./bundle/chunk-ZQT6OPVH.js	3.62 MB	+3.62 MB (new file)	🆕
./bundle/core-SQVWB6HG.js	40.3 kB	+40.3 kB (new file)	🆕
./bundle/devtoolsService-BB2XUIA2.js	27.7 kB	+27.7 kB (new file)	🆕
./bundle/interactiveCli-MCDAKWKJ.js	1.59 MB	+1.59 MB (new file)	🆕
./bundle/oauth2-provider-KOTTOV6L.js	9.19 kB	+9.19 kB (new file)	🆕

ℹ️ View Unchanged

Filename	Size
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[abhipatel12]

/gemini review

[gemini-code-assist]

Code Review

This pull request aims to fix a bug where user-defined MCP server settings were ignored for servers provided by extensions, by merging user configurations with extension settings. While the changes in mcp-client-manager.ts correctly handle merging logic, including the unioning of tool lists, and are supported by thorough tests and updated documentation, this PR introduces two high-severity security issues. Specifically, the union of tool allowlists weakens user-defined security restrictions, and a race condition during initialization can lead to the wipeout of extension-defined security controls and the creation of zombie processes. These critical security concerns must be addressed.

[abhipatel12]

/gemini review

[gemini-code-assist]

Code Review

This pull request correctly addresses an issue where user settings for extension-provided MCP servers were being ignored. The new mergeMcpConfigs function and the updated logic in maybeDiscoverMcpServer enable proper merging of user and extension configurations. The accompanying documentation and tests are thorough. However, I've identified a critical issue in the new merge logic that could cause user overrides for specific connection properties to be ignored. Please see my detailed comment.

[abhipatel12]

/gemini review

[gemini-code-assist]

Code Review

This pull request correctly addresses a bug where user-defined MCP server settings were being ignored for servers provided by extensions. The new implementation introduces a robust merging logic that correctly prioritizes user configurations over extension defaults for scalar properties and environment variables, while securely merging tool inclusion/exclusion lists. The changes are well-tested, covering different loading orders and edge cases, and the accompanying documentation update clearly explains the new override behavior to users. The implementation is clean and effective.