files_transaction_prepare(): don't leak flags to packed transaction

The files backend uses `ref_update::flags` for several internal flags. But those flags have no meaning to the packed backend. So when adding updates for the packed-refs transaction, only use flags that make sense to the packed backend. `REF_NODEREF` is part of the public interface, and it's logically what we want, so include it. In fact it is actually ignored by the packed backend (which doesn't support symbolic references), but that's its own business. Signed-off-by: Michael Haggerty <mhagger@alum.mit.edu> Signed-off-by: Junio C Hamano <gitster@pobox.com>