Add indexes in generated protobuf

The protobuf logic will mark an entire table as indexed, but that may not line up to what we need.

The usage of the Indexed annotation on the message indicates that custom IndexedField annotations will be used to selective enable indexes.

This is true whether the cache is marked as indexed (which would be specified in the cache template) or not.

If we auto-create an indexed cache, then all fields are automatically indexed and there's no need for the indexed annotation.