Git won't catch new files the agent is adding. To get around that you can of course always add all new files, but then you'll potentially have your repo polluted with a bunch of temporary scratch files instead.

You can typically go back and edit git history. But it will require force push and breaking changes. And a few sacrifices to ensure that it doesn't make a mistake because then your repo is potentially broken.

Best way to do that is probably to have it work on branches and then squash merge those.