Rename app.new_window to app.new-window

Underscores should not appear in action names.

https://bugzilla.gnome.org/show_bug.cgi?id=721952
preferences: associate the window with the app

This allows the app to stay open if the preferences window is open.

Also, allow the preferences window to be created without a transient
window for it to be associated with.

Make sure we never return the preferences window as the active window.

https://bugzilla.gnome.org/show_bug.cgi?id=721952