application-actions: use valid window list

We were using the internal list of the application to
iterate through the windows and closing them.
Problem is that when closing one window, the list is modified,
so next time accessing the list we are accessing the "old"
list, which is invalid and makes nautilus crash.

To fix it make a copy of the list to preserve the consistency.

https://bugzilla.gnome.org/show_bug.cgi?id=755803