git will check the .git folder, find a hook, and run it where it is applicable. If you are cloning a remote repository may inherit you with malicious hooks. These hooks run before you git operations, for example it is useful if you want lint the code a certain way before pushing, it does it automatically.

You can disable this behavior globally. Yes, the agent should have no git access this way, however you could always do a local sub repository if you want to. You track your changes twice, but should work