Explore how to pass the “inner” provenance information to CWLProv/RO-Crate

[mr-c]

For the rdtLite (R script) provenance @simleo suggests

 {
	"@id": "prov.json",
    "type": "File",
    "conformsTo": "https://github.com/End-to-end-provenance/ExtendedProvJson/blob/master/JSON-format.md",
    "name": "RDataTracker Provenance"
}

I believe the prov output from rdtLite is a mixture of their own terms on top of plain PROV-O, so it would be nice to indicate that the document conformsTo both specs.

On the CWL side we can either use the cwl.output.json to add the extra annotation, or perhaps add another field to the relevant section in outputs. But we'll need to make sure that this "inner" provenance is connected with the specific CommandLineTool execution, not the whole workflow.