Cleanup packs

[pgrete]

  std::vector<parthenon::MetadataFlag> flags_ind({Metadata::Independent});
  auto cons_in = md->PackVariablesAndFluxes(flags_ind)

is currently used in many places (followed by fixed indices).
This may cause issue in case there are more Metadata::Independent fields.
Thus, the logic should be updated to only pull the required vars.