protocol: Add deprecation note about wl_shell

Now that xdg_shell is stable and much better defined than wl_shell we
can finally deprecate wl_shell and guide users towards xdg_shell
instead.

Signed-off-by: Jonas Ådahl <jadahl@gmail.com>
Acked-by: Pekka Paalanen <pekka.paalanen@collabora.co.uk>
Reviewed-by: Daniel Stone <daniels@collabora.com>