setup-etc.pl: Keep track of copied files

We now track copied files in /etc/.clean. This is important, because
otherwise files that are removed from environment.etc will not
actually be removed from the file system. In particular, changing
users.extraUsers.<user>.openssh.authorizedKeys.keys to an empty list
would not cause /etc/ssh/authorized_keys.d/<user> to be removed, which
was a security issue.