core: Ensure we clean up leftover directories during merge
core: Ensure we clean up leftover directories during merge

(Not sure why this regressed)

resin-io/ostree,gatispaeglis/ostree,gatispaeglis/ostree,GNOME/ostree,resin-io/ostree,resin-io/ostree,sujitfulse/ostree,sujitfulse/ostree,gatispaeglis/ostree,gatispaeglis/ostree,leandrosansilva/ostree,sujitfulse/ostree,GNOME/ostree,resin-io/ostree,sujitfulse/ostree,gatispaeglis/ostree,leandrosansilva/ostree,leandrosansilva/ostree,GNOME/ostree,leandrosansilva/ostree,leandrosansilva/ostree,sujitfulse/ostree,resin-io/ostree,GNOME/ostree,gatispaeglis/ostree,GNOME/ostree