window-tracker: Fix memory leak

shell_window_tracker_get_window_app() returns a new reference
which we need to drop once we're done.

https://bugzilla.gnome.org/show_bug.cgi?id=722927
overview: Fix DESKTOP clone position

The DESKTOP window might not be located at (0,0), in particular
on multi-monitor setups. While we already consider this by setting
the clone's position, we then stuff the clone into a container which
ignores it - meh ...

https://bugzilla.gnome.org/show_bug.cgi?id=723306