window: Update popover positions on ::size-allocate

Popovers may get relocations optimized away if only x/y changed
in the GtkAllocation. So make sure the toplevel updates popover
positions on all situations.

https://bugzilla.gnome.org/show_bug.cgi?id=729140
Don't forget to allocate popovers

When GtkApplicationWindow has a menubar, we don't chain up
to the GtkWindow size_allocate, which used to position the
popovers. Move that to _gtk_window_set_allocation() which
is always called by GtkApplicationWindow.

https://bugzilla.gnome.org/show_bug.cgi?id=736205