To install:
$ git clone --recursive git://github.com/matthisamoto/dotfiles.git ~/.dotfiles
$ ~/.dotfiles/scripts/install.sh
The installer will never delete a file from your $HOME directory. If it encounters a file that isn't a symlink, it lets you handle the situation.
To uninstall:
$ ~/.dotfiles/scripts/uninstall.sh
This will only remove files of interest from $HOME that are symlinks.