drop pack.py in favor of cwl_utils.pack

[mr-c]

Only 7 test failures!

• all CWL documents are first upgraded to CWL v1.2 (or whatever cwl-upgrader thinks is "latest"); this is a big change in behavior
  • reasoning: to hand mixed versions cleanly...

Aim to address #1728

[codecov]

Codecov Report

Merging #1730 (cbc0a69) into main (2a2216b) will decrease coverage by 10.90%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##             main    #1730       +/-   ##
===========================================
- Coverage   66.60%   55.70%   -10.91%     
===========================================
  Files          89       44       -45     
  Lines       15854     7750     -8104     
  Branches     4190     1990     -2200     
===========================================
- Hits        10560     4317     -6243     
+ Misses       4206     2909     -1297     
+ Partials     1088      524      -564     

Impacted Files	Coverage Δ
cwltool/cwltool/job.py	61.46% <0.00%> (-0.99%)	⬇️
cwltool/main.py
cwltool/validate_js.py
cwltool/docker.py
cwltool/workflow.py
cwltool/provenance_constants.py
cwltool/load_tool.py
cwltool/singularity_utils.py
cwltool/docker_id.py
cwltool/mutation.py
... and 36 more

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[mr-c]

Some of the test failures are due to slightly different behavior in cwl_utils.pack (which is derived from sbpack's cwlpack)

• it puts step processes inline instead of in a $graph.
• therefore the id fields are not prefixed with their original step names

Other test failures might be due to errors in cwl_utils.pack itself

• not including all $schemas in the parent $schemas

[lgtm-com]

This pull request fixes 3 alerts when merging 8af88ce into 2a2216b - view on LGTM.com

fixed alerts:

• 3 for Module-level cyclic import

[lgtm-com]

This pull request fixes 3 alerts when merging cbc0a69 into 2a2216b - view on LGTM.com

fixed alerts:

• 3 for Module-level cyclic import