Bug: run_shell_command fails with 'Cannot read properties of undefined (reading \'publish\')'

### What happened?
When Gemini CLI attempts to run `git checkout` or `git branch` commands via the `run_shell_command` tool, it fails with an internal tool error: `Cannot read properties of undefined (reading 'publish')`. This happens consistently for branch creation/switching commands.

### What did you expect to happen?
The tool should execute the shell command (`git checkout -b ` or similar) successfully and return the command output.

### Client information

Client Information

macOS
gemini-cli-core 0.35.0-nightly

### Login information
n/a

### Anything else we need to know?
This error is blocking automated PR creation workflows since the agent cannot create or switch to new branches when trying to use the GitHub Issue/PR creator skills.