In a true dropbox-like fashion, I tried to import my entire homefolder into the git-annex assistant. However, it seems that git-annex breaks on the several git repositories I've got checked out in my "Projects" folder. Is this a possible use case, or should I look at other tools to perform this with?
The assistant is not ready to manage whole home directories, and the webapp refuses to allow you to do that.
git doesn't allow checking a git repository into a git repository either. I archive old git repos inside one of my annexes by tarring them up.