Implement cwltool:Loop extension for CWL runner (#4227)

[annagiroti]

Changelog Entry

Implement cwltool:Loop extension for Toil's CWL runner, adding iterative loop execution, outputMethod: all accumulation, and full LoopInput feature support (loopSource, linkMerge, pickValue, default, valueFrom) with a configurable iteration limit via --cwl-loop-iteration-limit.

Resolves #4227

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[adamnovak]

This looks pretty good, but I think it could be simplified.

We should be able to pull most of the test files from the packaged data files of our cwltool dependency.

And I think we can get away with not adding either LoopOutputSource (because Toil promises can already do a dict key lookup) or LoopStepValueFrom (because StepValueFrom can be generalized to cover both cases by adding an optional parameter and a conditional).

[adamnovak]

This looks good to me!