xdg-shell: Popups should be placed relative to the parent surface

According to the xdg-shell protocol specification the (x, y) coordinates
passed when creating a popup surface is relative to top left corner of
the parent surface, but prior to this patch, if the parent surface was
a xdg_surface, it'd position it relative to top left corner of the
window geometry of that xdg_surface.

https://bugzilla.gnome.org/show_bug.cgi?id=749716