Allow for command line outdir specification

[theferrit32]

Let user specify an outdir for the datacommons workflow execution, so that output files can be sent to a different subdirectory of the shared filesystem.

Require that the output directory is a subdirectory of the base directory for the job.

So for example of the job is executed with:
$ cwltool --data-commons myworkflow.cwl /renci/irods/workflowjob1.yml

allow for the outputs from the workflow to be placed in a subdirectory like:
$ cwltool --data-commons --outdir=/renci/irods/workflowjob1_out myworkflow.cwl /renci/irods/workflowjob1.yml

Which would result in input files being read from /renci/irods and output files being placed in /renci/irods/workflowjob1_out