When an app directory (i.e. `/home/dokku/myapp`) is created before the
app is pushed for the first time (which may occur if config files such
as `ENV` are added before the initial push), then the app directory will
not be initialized to a bare git repo nor will the pre-receive hook be
installed because `plugins/git/commands` assumes that if `$APP_PATH`
exists, then the directory must also be git initialized too. This fix
checks for `$APP_PATH/refs` instead.
HOME is not consistent if dokku is ran e.g. as root (for setup).
The DOKKU_ROOT variable will also make it possible to have the repositories stored in an arbitrary location (works-ish right now)