shell-app: Track all application windows

Filtering out "non-interesting" windows beforehand as we currently do
means that we may get properties that should be based on all windows,
like the last time the application was used, wrong.
Just track all windows and filter out non-interesting windows manually
in the one place we actually care about the difference.

https://bugzilla.gnome.org/show_bug.cgi?id=719824