Clean up gmxfio includes

Clean up gmxfio includes

- Move xdr writing routines to gmxfio-xdr.h, to make it match the source
  file that implements them.  Include the new header where necessary.
- Remove gmx_fio_checktype() and replace with asserts in the xdr
  routines.
- Remove unnecessary gmxfio.h includes.  In particular, remove it from
  headers to not get it transitively to unrelated source files.
- Fix compilation that was broken by relying on transitively included
  headers (mostly cstringutil.h and futil.h) that no longer come through
  the transitive gmxfio.h.
- Some minor cleanup elsewhere, in particular hiding functions from
  headers and fixing a few uses of mismatching file open/close
  functions.

Change-Id: Ic5366a23a421cfec82a518caee772e2bb53e8303