shell: Ignore non-toplevels for ShellWindowTracker::tracked-windows-changed
Popups and other override-redirect windows are meaningless to everything that depends on the ShellWindowTracker. Ignoring those windows will result in less ShellApp::windows-changed signal emissions, and less activity in the AppMenuButton and everything else that depends on them.
Reduces gnome-shell CPU activity while typing on the Epiphany addressbar, as the pop up animation there results in a number of xdg_popup being created and destroyed.