If a window is overlapped by a layered (i.e. partially transparent)
window then that region will not disappear from the native window clip
region. This lets us handle compositing multiple layers of windows.

For native subwindows this doesn't really work. For them we apply the
clip region as a shape to the native window which lets us have client
side windows overlapping the native window. However, with the addition
of the layered stuff the "overlapped-by-alpha-csw" part got broken, as
this area is not removed from the clip region of the native window.

We fix this by also removing the layered area when applying the shape.
This means alpha and alpha backgrounds don't work over native windows,
but there is not much to do about that.

https://bugzilla.gnome.org/show_bug.cgi?id=696370