Move types/ishift.h to pbcutil/

- Remove the include from typedefs.h, and add it to files that are using
  it.

Change-Id: I752648c73ba767eff30c113c84aabd5c7d7494ac
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