Fix edge case: app directory is created before first app push

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.

This issue appeared in https://github.com/fgrehm/chef-dokku/issues/11.