Simplified handling of simulation runners

Simplified handling of simulation runners

Argments to runners are now passed via struct members. That struct is
expected to change over the medium term, as most of its contents
should either be in a container of modules, or data with such a
module. As such, it does not make sense to do a lot of coding to
manage its contents in a sound way. The practical effects of using
this struct are almost the same as the old approach of passing a
forest of arguments - some variables are declared in a scope,
initialized with values, then used once.

The form is chosen so that
* the do_md() etc. functions do not need a large number of useless
  textual changes now
* future changes to names and types of the former parameters do not
  need to be edited in matching way in multiple places of code and
  their doxygen
* we don't need to mark things gmx_unused anywhere

Useless unchecked return values have been removed.

Some excessive includes in integrator.h were removed, which
generates a few minor fixes elsewhere.

Refs #1793

Change-Id: I678598175192c9c68113fdd79fcee17f8e5c504e