Claude Code gives you three layers, and they do different jobs. Deny rules in settings.json stop its own file reading and the commands it recognises, such as cat, from touching .env, but its permissions page warns that they do not stop a Python script that opens the file itself. The sandbox does. Turned on in settings, it runs every shell command inside macOS's own sandbox, where a denyRead entry blocks .env files for every program the agent starts and a credentials entry unsets variables such as GEMINI_API_KEY before each command runs. Ask rules add the third layer, a prompt before the render script runs, which even auto mode cannot skip.
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