Remove more uses of typedefs.h

- Replace typedefs.h with individual headers and/or forward
  declarations, with focus on headers and code outside
  gmxlib/mdlib/gmxana/gmxpreprocess.
- Remove unused dlb.h.
- Fix some source files that were relying on transitive includes.

Change-Id: Icf32798d664f6753eb0c0cb2a88e178bc21c9d78
Move mtop_util.* and topsort.* to topology/

- Remove unnecessary includes of these headers.
- Some minor cleanup in the moved files.

Change-Id: I7ad70f4c1870307713db35b8b243bed1dc9cbdd2