move model step overall settings to model step yaml file

[bstabler]

All the model step settings should be in the model step yaml files. For example, move aggregate_zone_file_names from settings.yaml to aggregate_zone.yaml.

[toliwaga]

The file names in settings that are used in the tables injectables should maybe go in a tables.yaml file as it is not easy to figure out where, for example, the various zone file lists should go.

For now, I put the file lists for things like aggregate_id_matrices in aggregate_od.yaml, but some might argue all file lists should go in the same place?