I think no one has mentioned rcm[1]. I just maintain a private git repository cloned in .dotfiles in each system I own, and use rcm to set up symbolic links properly. It works pretty well with directories and lets you choose between creating and populating it with symlinks, or just symlinking the whole directory. For example, I can symlink the full .vim directory (including git submodules) and only link some files inside the .ssh directory (link the config file to my .dotfiles repo but leave ssh keys alone).

1: https://robots.thoughtbot.com/rcm-for-rc-files-in-dotfiles-r...