Remove sysstuff.h includes from headers

Remove sysstuff.h includes from headers

Remove #include "sysstuff.h" from all headers, and replace it with
standard headers where necessary.  Add necessary standard headers to
source files that previously got them transitively from one of these.

Use snew() in gmx_spatial.c instead of a custom implementation.
Replace some free() with sfree().

Part of getting rid of sysstuff.h.

Change-Id: I857ba69c004aea16195e629c5bf69df32724b3fc