guix system: Make 'init' idempotent again.

This fixes a regression introduced in
df2f6400: since the new
'register-path' (actually 'reset-timestamps') would make files
read-only, 'delete-file-recursively' would fail to delete them.  Thus,
re-running 'guix system init' on an already-populated store would fail
with a 'delete-file' EPERM.

* guix/scripts/system.scm (copy-item): Use 'lstat' instead of
'file-exists?'.  Call 'make-file-writable' on each directory below
DEST.