You don't have to regenerate a zipfile each time you do something - the zipfile is just to give a single file for distribution. It's just a zip of the directory.

Git is supported in the spec, though the tool doesn't yet handle it (soon! git is nice as you get a log "for free" which helps agents understand more about the memories).

As for sqlite in git: yes you can gitignore it, you could use git-lfs, you could use an out of band database. It would be great if there were another format more amenable to git to store vectors in. I looked at csv closely, but I was worried about float formatting/representational bugs. There is a gap in the market for a format here.