This is my ideal setup for a Unix/Linux environment. I've taken things from all over the place, and I can't guarentee it will work on your machine as well as it does on mine - this is just what works for me.
Run rake install inside the repo.
This will install Janus, sync git submodules for vim plugins (in ~/.janus), then symlink all of the config files from the repo into your home directory.
If the installer finds an existing file when symlinking, it will prompt you to: overwrite it, back it up (moved to a temp folder, which can be restored when 'uninstalling'), or skip it.
Run rake uninstall inside the repo.
This will remove all of the symlinks and restore any backed up files.
You can run rake brew which will install all the packages listed
in the Brewfile. Not recommended.
To add more vim plugins, do a git add submodule https://github.com/... in the /janus folder, and they will automatically load the next time you run vim.