I find I keep the git add to the be one thing I keep track of (in production services, if not throw-away or non-prod visualization vibe coded things). I've never even used git add . - I git diff each file one by one, and git add them in one by one. It's needed to prevent my own errors, and it's needed to keep some model of what the AI is doing in my mind. Now, I myself don't do much commenting in line; I tended to rely on good names, good function comments, good module descriptions as comments at the top of a file; for the flow, I would log a lot and hopefully the failure/success logs made the thinking clear for what is going on and why. But I let the AI keep all its comments, till they crowd out the code at least.

Replying to a comment below (on shell scripts), I use it for shell scripts, python "get this data and slice it in these ways" and elisp, all the time. 30 seconds to get and answer instead of 30 minutes. Being able to do them in 30 minutes took a lot of skill and practice, but the pleasure of finishing that for an ad hoc thing when I really just want the data output is something I can give up.