refactor(cli): fix settings merging so that settings using the new json format take priority over ones using the old format

[jacob314]

Summary

Legacy settings were taking priority over the new setting syntax when merging which is surprising behavior.

Details

Fixed so that new settings take priority over legacy and tried to simplify merging logic a little bit by removing special cases that aren't needed.

Related Issues

This make fix #14807

How to Validate

Define a mix of old and new format settings in your settings.json. Verify that the new format settings take priority.

[gemini-code-assist[bot]]

Summary of Changes

Hello @jacob314, I'm Gemini Code Assist[^1]! 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 enhances the robustness and security of the configuration merging logic. It refines the deepMerge utility to prevent prototype pollution by explicitly blocking __proto__ while allowing other special properties like constructor and prototype to merge correctly. Furthermore, it addresses a critical issue in the settings migration process, ensuring that newer V2 settings reliably take precedence over older V1 settings, thereby eliminating 'zombie setting' conflicts. These improvements are thoroughly validated with new test cases covering various merge scenarios and migration behaviors.

Highlights

• Refined Deep Merge Security: The deepMerge utility now specifically blocks only the __proto__ property from being merged to prevent prototype pollution, while allowing constructor and prototype to be merged if they are legitimate own properties.
• Undefined Value Handling: The deepMerge function has been updated to ignore undefined values in the source object, ensuring they do not overwrite existing defined values in the target object during a merge operation.
• V1 to V2 Settings Migration Fix: A 'zombie setting' bug in the V1 to V2 settings migration process has been resolved. V2 settings will now correctly override V1 settings, preventing older configurations from inadvertently interfering with newer ones.
• Comprehensive Test Coverage: New and updated test cases have been added to validate the refined deepMerge behavior, including scenarios for primitive-to-object and object-to-primitive overwrites, and to confirm the correct precedence of V2 settings during migration.

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[github-actions[bot]]

Size Change: +191 B (0%)

Total Size: 21.6 MB

ℹ️ View Unchanged

Filename	Size	Change
./bundle/gemini.js	21.6 MB	+191 B (0%)
./bundle/sandbox-macos-permissive-closed.sb	1.03 kB	0 B
./bundle/sandbox-macos-permissive-open.sb	890 B	0 B
./bundle/sandbox-macos-permissive-proxied.sb	1.31 kB	0 B
./bundle/sandbox-macos-restrictive-closed.sb	3.29 kB	0 B
./bundle/sandbox-macos-restrictive-open.sb	3.36 kB	0 B
./bundle/sandbox-macos-restrictive-proxied.sb	3.56 kB	0 B

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