fix(cli): fix special paths in workflow files and bump toil/cwltool

[Panaetius]

closes #3455

cwl-utils changed the logic for calculating relative paths of steps where without a file:// scheme it made all paths relative to the current working dir, which differs from the path the workflow file is at.

Workflows/renku status didn't work with filenames like test<>b&c\\d .csv, as git returned them quoted

[coveralls]

Pull Request Test Coverage Report for Build 5142089880

• 10 of 12 (83.33%) changed or added relevant lines in 4 files are covered.
• 23 unchanged lines in 8 files lost coverage.
• Overall coverage increased (+0.09%) to 85.375%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
renku/core/migration/m_0005__2_cwl.py	4	5	80.0%
renku/infrastructure/repository.py	2	3	66.67%

Files with Coverage Reduction	New Missed Lines	%
renku/core/workflow/activity.py	1	93.93%
renku/ui/cli/init.py	1	96.9%
renku/ui/cli/service.py	1	68.91%
renku/ui/service/errors.py	1	82.54%
renku/infrastructure/repository.py	2	81.5%
renku/ui/service/views/error_handlers.py	2	87.07%
renku/core/util/git.py	5	85.07%
renku/core/migration/models/v9.py	10	80.31%

Totals
Change from base Build 5141817213:	0.09%
Covered Lines:	25826
Relevant Lines:	30250

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💛 - Coveralls