Address review comments (WIP) [skip ci]

Adresses various review comments and largely purges JSON from
metadata.py.

TODO:

- Document the purpose of from/to_dict in the module header or in each
  function header?
 something along the lines of:
  "Dictionary utility methods, to e.g.:
   - facilitate default JSON de/serialization
   - allow easy comparision of metadata objects""
- Proof read (against CR comments)
- Split this commit + commit messages
- Ping reviewers