I synchronize home directories on a couple of machines using unison. Is there a recommended way to do the equivalent using git-annex?
There are a few problems you are likely to run into if you try to store everything in git-annex:
For these reasons, I currently encourage users to use one or more git-annex repositories to store and sync whatever large data files they need, but to confine this to subdirectories of the home directory. There are other tools like vcsh that are better suited to storing things like dotfiles in git, rather than using git-annex for that. And other tools like mr can make it easy to work with a set of repositories, so you can have your dotfiles stored in one or more repositories and your large files in others and update them all with one command.
See http://vcs-home.branchable.com/ for more on this..