Discard undeclared fields from cwl.output.json

[GlassOfWhiskey]

This commit discards all fields that are present in a cwl.output.json file but have not been declared in the outputs section of the related CommandLineTool, implementing common-workflow-language/cwl-v1.3#80.
Conformance tests for this update have been implemented in common-workflow-language/cwl-v1.3#81.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.13%. Comparing base (766d58b) to head (dbfbfab).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2177      +/-   ##
==========================================
+ Coverage   85.10%   85.13%   +0.02%     
==========================================
  Files          46       46              
  Lines        8358     8368      +10     
  Branches     1951     1956       +5     
==========================================
+ Hits         7113     7124      +11     
  Misses        779      779              
+ Partials      466      465       -1     

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[mr-c]

• Add something like if ORDERED_VERSIONS.index(self.metadata[ORIGINAL_CWLVERSION]) >= ORDERED_VERSIONS.index("v1.3.0-dev1"): to only change behavior for CWL v1.3.0+
• add tests here for the previous behavior using cwlVersion: v1.0, cwlVersion: v1.1, and cwlVersion: v1.2

[GlassOfWhiskey]

@mr-c as I wrote in the CWL v1.3 spec, I assumed undefined behavior for previous CWL versions, meaning that any implementation is free to do whatever it wants. Therefore, I am completely against putting conformance test for an undefined behavior just because cwltool did something, also because I am not sure what other implementations do in this particular use case.

[mr-c]

@GlassOfWhiskey I agree, I was asking for tests in cwltool, not new conformance tests. That way we don't break anything for cwltool users running a CommandLineTool directly. For CWL workflows I don't think there is a way to make use of the undeclared outputs, beyond them showing up in logs & provenance reports.