Clean up logging and output from pods and calrissian process

[johnbradley]

Currently a JSON object is printed to stdout which contains details about the files created in the job.
This data can be see in the logs but it is mixed with stderr.
These two data(stdout and stderr) should be persisted is some way outside of the job logs.

[dleehr]

Additionally, the above stderr is currently only the operational logging messages that calrissian reports in its logic. The logs from individual CWL CommandLineTools that contain the bulk of the important workflow information are not fetched from the pods.

cwltool by default prints these tool output streams (stdout/stderr) to cwltool's stderr. Unless we have a better idea, we should mirror that behavior.

[dleehr]

And add a command-line argument to "also write your logs to this file"