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fix(cli): preserve manually added configurations in settings.json#25927

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fix/preserve-manual-settings-23138
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fix(cli): preserve manually added configurations in settings.json#25927
cynthialong0-0 wants to merge 2 commits into
mainfrom
fix/preserve-manual-settings-23138

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@cynthialong0-0 cynthialong0-0 commented Apr 24, 2026

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Summary

Fixes bug where manually added configurations in settings.json (e.g., hooks) were wiped whenever settings were saved via the CLI (like toggling a theme).

Details

The applyKeyDiff function in commentJson.ts used "sync-by-omission" semantics, which explicitly deleted any key in the file not present in the CLI's in-memory settings object. Since unknown or manually added keys are often missing from this object, they were lost on every save.

This PR refactors applyKeyDiff to be additive. It now preserves existing keys unless they are explicitly set to undefined in the update object. Migration logic in settings.ts and the gemini mcp remove command have been updated to use undefined as the explicit deletion signal.

Related Issues

Fixes #23138

How to Validate

  1. Manually add a non-schema key to your settings.json (e.g., "hooks": { "onStartup": ["echo test"] }).
  2. Run the CLI and toggle a setting (e.g., theme).
  3. Verify that the manually added key is still present in settings.json.
  4. Run npm test -w @google/gemini-cli -- src/utils/commentJson.test.ts to verify the automated tests.

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
      • npx
      • Docker
      • Podman
      • Seatbelt
    • Windows
      • npm run
      • npx
      • Docker
    • Linux
      • npm run
      • npx
      • Docker

@cynthialong0-0 cynthialong0-0 marked this pull request as ready for review April 24, 2026 17:22
@cynthialong0-0 cynthialong0-0 requested a review from a team as a code owner April 24, 2026 17:22
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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 addresses a bug where manually added configurations in settings.json were inadvertently removed when the CLI saved settings. By shifting from a 'sync-by-omission' approach to an additive model, the system now preserves existing keys by default. Deletions are now handled explicitly by setting a key to undefined, ensuring more predictable and safer configuration management.

Highlights

  • Additive Configuration Updates: Refactored the applyKeyDiff function to adopt additive semantics, ensuring that manually added configurations in settings.json are preserved instead of being deleted during CLI updates.
  • Explicit Deletion Signal: Introduced undefined as the explicit signal for deleting keys, updating migration logic and the gemini mcp remove command to utilize this new pattern.
  • Test Suite Updates: Updated existing tests and added new test cases to verify that nested objects are preserved and that keys are only removed when explicitly set to undefined.
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@gemini-cli gemini-cli Bot added priority/p1 Important and should be addressed in the near term. area/core Issues related to User Interface, OS Support, Core Functionality labels Apr 24, 2026
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github-actions Bot commented Apr 24, 2026

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Size Change: -32 B (0%)

Total Size: 33.7 MB

Filename Size Change
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ℹ️ View Unchanged
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Code Review

This pull request refactors the configuration synchronization logic to ensure that settings are only deleted when explicitly set to undefined, rather than being removed when omitted. This change prevents the accidental wiping of manually added or unknown configuration keys. The updates span the MCP server removal command, settings migration logic, and the core applyKeyDiff utility, supported by updated test cases. Feedback was provided to use object spread syntax instead of direct mutation when updating the MCP servers configuration to improve code consistency and avoid side effects.

Comment thread packages/cli/src/commands/mcp/remove.ts Outdated
@cynthialong0-0 cynthialong0-0 added priority/p2 Important but can be addressed in a future release. priority/p1 Important and should be addressed in the near term. and removed priority/p1 Important and should be addressed in the near term. priority/p2 Important but can be addressed in a future release. labels Apr 24, 2026
Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com>
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/gemini review

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Code Review

This pull request modifies the settings management logic to prevent accidental deletion of configuration keys. Instead of removing keys that are omitted from the update object, the system now requires keys to be explicitly set to undefined to be deleted. This change is implemented in the applyKeyDiff utility and applied across MCP server removal and settings migration logic. The test suite has been updated to verify that omitted fields are preserved while explicit undefined values trigger deletion. I have no feedback to provide.

@sripasg sripasg added the size/m A medium sized PR label Jun 2, 2026
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area/core Issues related to User Interface, OS Support, Core Functionality priority/p1 Important and should be addressed in the near term. size/m A medium sized PR

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settings.json reset to defaults when system theme changes, deleting custom hooks

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