Remove old help formatting code

Remove old help formatting code

Make parse_common_args() format its help using the new
CommandLineHelpWriter class.  To support this:
 - Add conversion functions that map t_filenm and t_pargs options to
   corresponding Option classes.
 - Add support for arbitrary file types from the filenm.h enum to
   FileNameOption.
 - Add support for writing a list of known issues from
   CommandLineHelpWriter.
 - Some minor extensions to the Option classes to make it easy to do
   the conversion.
 - Fix gmx_hbond to not specify the same option twice.
 - Remove wman.* as unused after the change.

Related to #969.

Change-Id: I25143ddfa4226abd5ae5b95172f69c8fc615b720