feat: enable extensions to configure includeDirectories

[jsafyan]

Partially addresses #12634. Supersedes #12676.

Implements the context.includeDirectories configuration for extensions, allowing them to contribute to the CLI's context.

• Adds includeDirectories to GeminiCLIExtension and ExtensionConfig.
• Updates ExtensionManager to load and resolve these directories (supporting relative paths).
• Updates loadCliConfig to merge extension directories with user settings.
• Includes comprehensive tests for path resolution and precedence.

[gemini-code-assist]

Summary of Changes

Hello @jsafyan, 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 introduces a new feature that allows Gemini CLI extensions to configure includeDirectories. This enhancement enables extensions to specify directories that should be incorporated into the CLI's context, thereby expanding their ability to influence the CLI's behavior and access relevant files. The changes involve updating configuration interfaces, implementing robust path resolution within the extension manager, and integrating these extension-provided directories into the main CLI configuration, ensuring a seamless and extensible experience.

Highlights

• Extension Configuration: Extensions can now define includeDirectories within their context configuration, allowing them to contribute specific directories to the CLI's operational context.
• Path Resolution: The ExtensionManager has been updated to load and correctly resolve these includeDirectories, supporting absolute, home-relative (~), and extension-relative paths.
• Configuration Merging: The loadCliConfig function now merges includeDirectories specified by active extensions with existing user settings and command-line arguments, ensuring proper precedence.
• Documentation and Testing: Documentation has been updated to reflect the new context.includeDirectories property, and comprehensive tests have been added to verify path resolution, merging logic, and the exclusion of inactive extension directories.

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[gemini-code-assist]

Code Review

This pull request adds the ability for extensions to specify includeDirectories to be added to the CLI's context. The implementation correctly handles path resolution for absolute, relative, and tilde-prefixed paths. The changes are well-tested. However, I've identified a security-related issue: the extension installation consent prompt does not inform the user about the directories an extension will add to the context. This should be addressed to ensure users are fully aware of an extension's capabilities before installation.

[bdmorgan]

Hi @jsafyan, thank you so much for your contribution to Gemini CLI! We really appreciate the time and effort you've put into this.

We're making some updates to our contribution process to improve how we track and review changes. Please take a moment to review our recent discussion post: Improving Our Contribution Process & Introducing New Guidelines.

Key Update: Starting January 26, 2026, the Gemini CLI project will require all pull requests to be associated with an existing issue. Any pull requests not linked to an issue by that date will be automatically closed.

Thank you for your understanding and for being a part of our community!

[gemini-cli]

Hi there! Thank you for your contribution to Gemini CLI.

To improve our contribution process and better track changes, we now require all pull requests to be associated with an existing issue, as announced in our recent discussion and as detailed in our CONTRIBUTING.md.

This pull request is being closed because it is not currently linked to an issue. You can easily reopen this PR once you have linked it to an issue.

How to link an issue:
Add a keyword followed by the issue number (e.g., Fixes #123) in the description of your pull request. For more details, see the GitHub Documentation.

Thank you for your understanding and for being a part of our community!