use the new TypeDict types from cwl-utils 0.41 more

[GlassOfWhiskey]

This commit checks that the new TypedDict type aliases specified in cwl-utils with PR common-workflow-language/cwl-utils#393 do not break anything in the cwltool type system.

[codecov]

Codecov Report

❌ Patch coverage is 89.68254% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.11%. Comparing base (55223a6) to head (a69a035).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cwltool/cwlprov/provenance_profile.py	80.00%	3 Missing and 2 partials ⚠️
cwltool/process.py	88.88%	1 Missing and 2 partials ⚠️
cwltool/command_line_tool.py	92.30%	0 Missing and 2 partials ⚠️
cwltool/cwlprov/ro.py	88.88%	0 Missing and 1 partial ⚠️
cwltool/load_tool.py	85.71%	0 Missing and 1 partial ⚠️
cwltool/utils.py	92.85%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2192      +/-   ##
==========================================
+ Coverage   85.10%   85.11%   +0.01%     
==========================================
  Files          46       46              
  Lines        8561     8567       +6     
  Branches     1993     1996       +3     
==========================================
+ Hits         7286     7292       +6     
  Misses        810      810              
  Partials      465      465              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

[mr-c]

Whoops, I forgot about this PR when I made #2225 ; here's an attempt to merge it all together