Move types/atoms.h to topology/

Move types/atoms.h to topology/

- Make all the structs forward-declarable, and use that in a few
  headers.
- Adjust existing few includes.
- Move functions that operate on these types from typedefs.[ch] to
  topology/ as well.

Nearly all code still depends on including this through
typedefs.h->types/topology.h, but that can wait.

Change-Id: If870711a061756a77451f52598d91e72d8948d92