desktop-shell: Do not leave views in layers upon shell destruction

This properly takes care of removing any of the views being added into
different layers upon shell destruction. Aggregates the shell_surface
destruction into one place to make things much more clearer. Keep  the
animation part only the weston_desktop_surface destruction rather than
doing it at shutdown.

Fixes #509.

Signed-off-by: Marius Vlad <marius.vlad@collabora.com>