Improve environmental variable caching

[stxue1]

PR to support environmental variable caching as mentioned here: DataBiosphere/toil#5187 (comment)

The structure of the preserve_environment code is roughly copied from a related function:

cwltool/cwltool/job.py

Lines 486 to 497 in 1b56338

	if runtimeContext.preserve_entire_environment:
	self._preserve_environment_on_containers_warning()
	env.update(os.environ)
	elif runtimeContext.preserve_environment:
	self._preserve_environment_on_containers_warning(runtimeContext.preserve_environment)
	for key in runtimeContext.preserve_environment:
	try:
	env[key] = os.environ[key]
	except KeyError:
	_logger.warning(
	f"Attempting to preserve environment variable {key!r} which is not present"
	)

[codecov]

Codecov Report

Attention: Patch coverage is 95.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.57%. Comparing base (2dce710) to head (0a2475c).

Files with missing lines	Patch %	Lines
cwltool/command_line_tool.py	83.33%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2101      +/-   ##
==========================================
- Coverage   84.74%   84.57%   -0.17%     
==========================================
  Files          46       46              
  Lines        8364     8377      +13     
  Branches     1961     1965       +4     
==========================================
- Hits         7088     7085       -3     
- Misses        807      818      +11     
- Partials      469      474       +5     

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[mr-c]

Thank you @stxue1 ; this will need some extra tests added to confirm your fixes

[mr-c]

Thanks for the extra tests! I see that they motivated some code changes :-)