Code clean-up in refs API implementation.

* mh/tidy-ref-update-flags:
  refs: update some more docs to use "oid" rather than "sha1"
  write_packed_entry(): take `object_id` arguments
  refs: rename constant `REF_ISPRUNING` to `REF_IS_PRUNING`
  refs: rename constant `REF_NODEREF` to `REF_NO_DEREF`
  refs: tidy up and adjust visibility of the `ref_update` flags
  ref_transaction_add_update(): remove a check
  ref_transaction_update(): die on disallowed flags
  prune_ref(): call `ref_transaction_add_update()` directly
  files_transaction_prepare(): don't leak flags to packed transaction