Create fileio module

Create fileio module

This patch contains only code motion. There are no functional code
changes. Moves lots of I/O code into src/gromacs/fileio. This means
lots of changes to avoid having everything as a compile-time dependency
of everything else because everything is pulled in via typedefs.h,
etc. Note that src/gromacs/legacyheaders/filenm.h and
src/gromacs/legacyheaders/types/filenm.h have been consolidated into
src/gromacs/fileio/filenm.h.

I/O code in files named stat*[ch] now lives in various new files in
fileio.

Files outside of the module now #include its header files in a proper
way, e.g. #include #include "../fileio/filenm.h" or
"gromacs/fileio/filenm.h" according to whether they are an installed
header, or not. Files within the module are blessed and do not need
that qualifier.

This module installs most of its headers (because they're almost all
inter-dependent; gmxfio_int.h is not installed because it is
only useful internally, vmdio.h is not installed because it
relies on a header from src/external)

Files in new module
* conform to preferred include-guard format.
* have up-to-date copyright headers thanks to Teemu's automatic
  script
* that are installed headers refer to other GROMACS include files via
  relative paths

Moves mdrun trajectory writing into wrapper function.

Removes small pieces of I/O code that was hiding behind "#if 0".

Some pieces of I/O code specific to the gmxpreprocess module have
remained there.

Moved a cppcheck suppression to follow matio.cpp to its new home.

Minor fix to xdrf.h logic, since it is now the subject of a CMake
test.

Refs #1292, #1193, #1137

Change-Id: I820036298d574966d596ab9e258ed8676e359184