Once a generalize test command is available and working with multiple engines #448 - allow all the same options for a new run command to supersede the old cwl_run command. It should cover both Galaxy and CWL artifacts and should be able to target the same backends as test (so Galaxy and cwltool at least, maybe more).

This will allow all the power of Galaxy's backend to be utilized but in a personalized matter. This should allow a bioinformatician for instance to easily run a pipeline on a Desktop or an HPC cluster. Usually it is an asset that Galaxy is a centralized web server - but there are times this level of coordination is a problem and all the extras are unwanted.