Interesting, but I think I'll stick with my own system[1]. I organize by task, not repo or program. Also I try to do a minimum of symlinking, instead relying on convention and PATH manipulation.
Edit: I don't mean to discourage you, by the way. The more variety in dotfile management the better.
[1]: http://bugsplat.info/2012-08-11-task-oriented-dotfiles.html