code coverage measurement: mismapped file paths

I tried to fix this in https://github.com/common-workflow-language/cwltool/pull/1609

but at https://github.com/common-workflow-language/cwltool/pull/1608#issuecomment-1027081283 we're still seeing the same path reported twice

> Impacted Files | Coverage Δ |  
> -- | -- | --
> cwltool/subgraph.py | 80.11% <85.00%> (-0.85%) |  
> cwltool/main.py | 71.67% <100.00%> (+0.13%) |  
> cwltool/cwltool/subgraph.py | 11.60% <0.00%> (-0.90%) |  
> cwltool/cwltool/main.py | 32.08% <0.00%> (ø) |  
> cwltool/cwltool/job.py | 62.32% <0.00%> (+0.78%) |