Create topology/atom_id.h

Create topology/atom_id.h

This was the only thing remaining in types/simple.h that still forced
some code to include it directly.  Remove most includes of
types/simple.h that were only including it for atom_id definition.
This removes some widespread dependencies on legacyheaders/, but does
not yet make any whole additional directories independent of them.

Change-Id: Ic3678bdb0160a820cf39157fc76ac21365cfb8dd