fix(config): treat system settings as read-only during migration and warn user #18277

spencer426 · 2026-02-04T05:20:15Z

Summary

This PR prevents the CLI from crashing when attempting to automatically migrate deprecated configuration settings in the system and system_default scopes. These scopes are now treated as
read-only, and the CLI will instead warn the user to perform manual updates for these files.

Details

Read-Only Enforcement: Modified LoadedSettings.setValue to automatically redirect any updates to System or SystemDefaults scopes to an in-memory-only store (setValueInMemory). This
prevents EACCES errors when the CLI doesn't have write permissions to system-wide configuration directories.
Migration Logic Update: Enhanced the migration functions to track deprecated flags found in system scopes. While migrations are still applied in-memory for the current session, the
changes are no longer persisted to disk for these specific scopes.
Actionable Warnings: Implemented a notification system using coreEvents.emitFeedback that alerts the user (in yellow) if their system configuration contains deprecated settings, listing
the specific flags that require manual intervention.

Related Issues

Fixes [UX] Failed to save to system_default scope while migrating deprecated settings. #18123

How to Validate

Create Mock System Config:
echo '{"general": {"disableUpdateNag": true}}' > /tmp/mock-system.json
Run Development CLI:
GEMINI_CLI_SYSTEM_SETTINGS_PATH=/tmp/mock-system.json npm run start
Verify Behavior:
- Confirm the CLI starts without crashing.
- Look for the yellow warning message: "The system configuration contains deprecated settings: [disableUpdateNag]. These could not be migrated automatically..."
- Verify that /tmp/mock-system.json has not been modified by the CLI.
Verify User Migration:
- Add a deprecated flag to your local ~/.gemini/settings.json.
- Run the CLI normally and verify that the local file is automatically updated.

Pre-Merge Checklist

gemini-cli · 2026-02-04T05:20:27Z

Hi @spencer426, 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-code-assist · 2026-02-04T05:20:34Z

Summary of Changes

Hello @spencer426, 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 significantly improves the robustness and user experience of the CLI's auto-update feature. By introducing both pre-flight permission checks and post-update command verification, it ensures that updates are performed reliably and that the CLI remains functional afterward. This proactive approach minimizes potential issues during the update process and provides clearer, actionable feedback to users in case of failure.

Highlights

Pre-flight Write Permission Check: Implemented a pre-flight check to verify write permissions in the executable directory before initiating auto-updates, preventing updates from failing due to insufficient permissions.
Post-update Command Verification: Introduced a post-update verification step to confirm that the 'gemini' command remains accessible in the system's PATH after a successful update, ensuring the CLI is still functional.
Improved Error Messaging: Enhanced error messaging for failed auto-updates, providing specific recovery instructions to the user, such as manual reinstallation commands.
Unit Test Coverage: Added comprehensive unit tests to cover the new pre-flight and post-update verification logic, ensuring the reliability of these new features.
Main CLI Integration: Integrated the auto-update check and handling directly into the main CLI execution flow, making the update process a seamless part of the user experience.

Changelog

packages/cli/src/gemini.tsx
- Integrated the checkForUpdates and handleAutoUpdate functions into the main main function, ensuring update checks occur during CLI execution.
- Added a catch block to silently handle and log errors from checkForUpdates in debug mode.
packages/cli/src/utils/handleAutoUpdate.test.ts
- Introduced mocks for node:fs and command-exists to facilitate testing of file system access and command availability.
- Updated test descriptions for clarity, specifically for nightly updates.
- Added new test cases to validate the behavior when pre-flight write permission checks fail and when post-update command verification fails.
- Modified the update-failed event handling test to assert that specific error messages are passed and displayed.
packages/cli/src/utils/handleAutoUpdate.ts
- Imported necessary modules: fs, path, commandExists, and debugLogger.
- Implemented a pre-flight check using fs.accessSync to ensure write permissions to the CLI's installation directory before an update attempt.
- Added a post-update verification step using commandExists.sync to confirm the gemini command is still in PATH after a successful update.
- Modified the handleUpdateFailed function to accept an optional message parameter, allowing for more descriptive error messages to be displayed to the user.

Activity

The author implemented pre-flight checks for write permissions to the executable directory.
The author added post-update verification to ensure the 'gemini' command remains in PATH.
The author improved error messaging for update failures, including recovery instructions.
The author added unit tests to cover the new verification logic.
The author integrated the update check and handling into the main CLI execution flow.

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github-actions · 2026-02-04T05:22:48Z

Size Change: +1.7 kB (+0.01%)

Total Size: 23.8 MB

Filename	Size	Change
`./bundle/gemini.js`	23.8 MB	+1.7 kB (+0.01%)

ℹ️ View Unchanged

Filename	Size
`./bundle/sandbox-macos-permissive-closed.sb`	1.03 kB
`./bundle/sandbox-macos-permissive-open.sb`	890 B
`./bundle/sandbox-macos-permissive-proxied.sb`	1.31 kB
`./bundle/sandbox-macos-restrictive-closed.sb`	3.29 kB
`./bundle/sandbox-macos-restrictive-open.sb`	3.36 kB
`./bundle/sandbox-macos-restrictive-proxied.sb`	3.56 kB

_{compressed-size-action}

gemini-code-assist

Code Review

This pull request introduces valuable pre-flight and post-update verifications for the auto-update feature, significantly enhancing its reliability. The implementation is solid, including corresponding unit tests. I've identified one area for improvement: a race condition in the non-interactive update check that could prevent it from running. My review includes specific suggestions to address this point.

packages/cli/src/gemini.tsx

jacob314 · 2026-02-05T22:49:31Z

packages/cli/src/config/settings.ts

    coreEvents.emitSettingsChanged();
  }

+  /**


there is too much duplicated logic with the regular setValue. We should just instead avoid saving the file if it is a system settings file

jacob314 · 2026-02-05T22:50:17Z

packages/cli/src/config/settings.ts

      if (modified) {
        loadedSettings.setValue(scope, 'general', newGeneral);
-        anyModified = true;
+        if (!isSystemScope) {


having system scope specific checks here is a little scary. why is this needed?

Refactored to use the SettingsFile interface to include a readOnly flag instead.

jacob314 · 2026-02-05T22:51:59Z

packages/cli/src/config/settings.ts


    // Migrate codebaseInvestigatorSettings -> agents.overrides.codebase_investigator
    if (experimentalSettings['codebaseInvestigatorSettings']) {
+      if (foundDeprecated) {


refactor so we don't have to repeat strings like codeBaseInvestigatorSettings in these migrate blocks. Add a shared helper.

Done. Combined setValue and setValueInMemory using a new helper that checks if a scope needs to be saved or just kept in memory. I also cleaned up the migration code to remove duplicate strings.

jacob314

…warn user (google-gemini#18277)

spencer426 requested a review from a team as a code owner February 4, 2026 05:20

spencer426 linked an issue Feb 4, 2026 that may be closed by this pull request

[UX] Failed to save to system_default scope while migrating deprecated settings. #18123

Closed

gemini-code-assist bot reviewed Feb 4, 2026

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packages/cli/src/gemini.tsx Outdated Show resolved Hide resolved

spencer426 force-pushed the fix/executable_path_#17881 branch 4 times, most recently from 95cb208 to 413e716 Compare February 5, 2026 21:58

spencer426 changed the title ~~fix(cli): add pre-flight and post-update verification for auto-updates~~ fix(config): treat system settings as read-only during migration and warn user Feb 5, 2026

jacob314 reviewed Feb 5, 2026

View reviewed changes

spencer426 force-pushed the fix/executable_path_#17881 branch 3 times, most recently from a9697c6 to cd6c338 Compare February 6, 2026 00:38

fix: treat system settings as read-only during migration and warn user

fb63f3b

spencer426 force-pushed the fix/executable_path_#17881 branch from cd6c338 to fb63f3b Compare February 6, 2026 00:44

spencer426 added 2 commits February 5, 2026 20:11

Merge branch 'main' into fix/executable_path_#17881

5ce68a1

Merge branch 'main' into fix/executable_path_#17881

a7843d6

jacob314 approved these changes Feb 6, 2026

View reviewed changes

spencer426 enabled auto-merge February 6, 2026 19:33

spencer426 added this pull request to the merge queue Feb 6, 2026

Merged via the queue into main with commit ad6d3fd Feb 6, 2026
26 checks passed

spencer426 deleted the fix/executable_path_#17881 branch February 6, 2026 19:45

aswinashok44 pushed a commit to aswinashok44/gemini-cli that referenced this pull request Feb 9, 2026

fix(config): treat system settings as read-only during migration and …

e31288c

…warn user (google-gemini#18277)

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How to Validate

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