gemini-cli - 💡(How to fix) Fix Gemini 3 Flash in Gemini CLI tried to discard my work when asked to commit the changes

What happened?

I usually spin up Gemini CLI and switch to YOLO mode to perform a /smart-commit which analyzes the changes in the working tree and creates multiple logical commits if the changes span distinct purposes.

Thankfully, I didn't, since Gemini ran git status, git diff and then tried to git checkout -p the files that were meant to be staged.

I mean WTH!!!! I ask to commit and it tries to discard??? Imagine the disaster I happened to avoid by accident mostly!!

Unacceptable!

What did you expect to happen?

I expected Gemini to commit my changes not attempt to discard them!!!

Client information

• CLI Version: 0.42.0
• Git Commit: 68e2196d5
• Session ID: cfa4ab75-23c7-4fbd-9d3b-5c06b42bd85a
• Operating System: darwin v24.11.0
• Sandbox Environment: no sandbox
• Model Version: gemini-3-flash-preview
• Auth Type: oauth-personal
• Memory Usage: 193.8 MB
• Terminal Name: Unknown
• Terminal Background: #212734
• Kitty Keyboard Protocol: Unsupported

Login information

Google account.

Anything else we need to know?

Gemini's report:

Incident Report: Critical Command Selection Failure

Incident Overview During a source control operation intended to stage and commit code, I executed a command that initiates the interactive discarding of local changes (git checkout -p) instead of the command for interactive staging (git add -p). This constituted a severe operational error that placed the integrity of the work at risk.

Technical Root Cause The failure originated from a confusion between two Git "patch" mode interfaces.

• Intent: To perform "surgical" staging, isolating specific changes within large files into separate logical commits.
• Action: I invoked the destructive variant of the patch interface, which is designed to revert uncommitted work to its last known-good state.

Impact and Risk Assessment The primary risk was the permanent loss of uncommitted logic. Had the command proceeded, it would have prompted for the removal of the very code I was instructed to preserve and commit. This represents a fundamental violation of the "Security & System Integrity" mandate, specifically regarding the protection of the source tree.