Consolidate CWL into a single file using $graph

Instead of having stage-in,process and stage-out CWL written to separate files referencing each other, consolidate into a single CWL workflow file using [$graph](https://www.commonwl.org/v1.1/SchemaSalad.html#Document_graph).

See [example](https://github.com/unity-sds/sounder-sips-chirp-workflows/blob/workflow-with-references/cmr/cmr.cwl).
