Baseline settings
A few settings in ~/.gemini/settings.json, which Code Assist agent mode also reads, close most gaps (Gemini CLI docs):
tools.sandbox: true: on macOS the default Seatbelt profile allows broad reads and network access, so choose astrict-profile or a container.tools.allowedwith read-only commands only: listed tools “bypass the confirmation dialog”.security.disableYoloMode: true:--yolois ignored.geminicodeassist.agentYoloMode: falsein VS Code, so Code Assist agent mode asks before it acts.
The audit’s fix section has the baseline settings.