shell-app: Fix a case where last_user_time isn't updated.

When activating an uninteresting window, the last_user_time isn't updated,
because we aren't tracking the window that the user_time gets updated on.
Hack around this by setting the last_user_time in shell_app_activate when
activating an uninteresting window.

https://bugzilla.gnome.org/show_bug.cgi?id=643302