Allow user to set arbitrary additional arguments to MooseRunner.set_run_opts()

[lukethehuman]

Add a generic kwarg to MooseRunner.set_run_opts to allow the user to add additional flags and arguments to the moose command as required. (For example the `--mesh_only`` flag.)

[lukethehuman]

Also for mpirun which is curently hardcoded to only use set options but many more options should be exposed to the user.