Fix some mdrun header dependencies

Fix some mdrun header dependencies

md_support.h, sim_util.h and update.h should not depend on each other
since any symbols they declare can be forward-declared by the others.

Updated some names for types - in particular, gmx_update_t is now a
struct, rather than an opaque pointer to a struct.

Also removed two orphaned function declarations used by the
now-removed SD2 integrator.

Change-Id: I84c0f8d7b90b5f68bbf940e5854834bb9d000c9f