Fix mdrun integration tests

Earlier code forced callMdrun() to trigger an mdrun -rerun, which was
not intended. Fixed that, and opened a path for code to use the
defaults of callMdrun(), but set up the executable name and prepend
command-line arguments to suit itself.

Ideally, the configurability would be more general, and there would
not be the requirement to specify the executable name, but so far this
is not a problem.

Change-Id: Id69927f9153a400455b728db577537ebc155d0af