Handle relative paths and locations in cwl.output.json

[tetron]

Conformance tests here:

common-workflow-language/cwl-v1.2#199

[codecov]

Codecov Report

Merging #1732 (c7cf662) into main (87f3b01) will increase coverage by 0.06%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1732      +/-   ##
==========================================
+ Coverage   66.54%   66.60%   +0.06%     
==========================================
  Files          89       89              
  Lines       15854    15856       +2     
  Branches     4157     4190      +33     
==========================================
+ Hits        10550    10561      +11     
+ Misses       4213     4206       -7     
+ Partials     1091     1089       -2     

Impacted Files	Coverage Δ
cwltool/command_line_tool.py	78.88% <100.00%> (+0.43%)	⬆️
cwltool/cwltool/command_line_tool.py	66.03% <0.00%> (+0.04%)	⬆️
cwltool/cwltool/singularity.py	51.94% <0.00%> (+0.43%)	⬆️
cwltool/cwltool/job.py	62.25% <0.00%> (+0.79%)	⬆️
cwltool/task_queue.py	77.04% <0.00%> (+1.63%)	⬆️

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