Made mdrun warn when generic kernels are used

mdrun now issues a warning if the generic group-scheme, or plain-C
Verlet-scheme kernels actually did some work. Such kernels should not
be called during routine use of mdrun.

It would be possible to do the check for the use of the generic
group-scheme kernel earlier in mdrun, but it's not easy to ensure we
only write the output at the first such step. Given that the group
scheme is deprecated, warning only at the end is sufficiently nice
behaviour.

Change-Id: Ib9b15165e53510f537687a4b448aaa01f1418522