Fix serialization

Fixes issues about serialization I brought up in an email.

There are three changes:
  1. cubbies when binary serializing do not care about the order in which keys were written to disk
  2. cubbies have versions, which the binary serializer (but not the mongo serializer) checks
  3. cubbies keep a set of which keys are valid, and the binary serializer won't only read keys which were store()d. This allows for deprecating keys.

These changes should probably be considered carefully, as they will break every single serialized file we have, but they should make it easier to move forward with serialization.