Fix codespell issues

[kinow]

I think codespell is failing in other PR's:

• Evaluate requirements and hints using the correct input reference #1703
• Changed outputSource refScope from 0 to 1 #1714
• Implementation of store RDF export of the workflow in CWL Prov RO-Bundle #1709

I tested it locally, and it reformatted a few files. I excluded the word ORE as that's from an ontology's name. After the changes in this PR, make cleanup passes with exit code 0 for me 🎉

(venv) kinow@ranma:~/Development/python/workspace/cwltool$ make cleanup
isort cwltool/argparser.py cwltool/builder.py cwltool/checker.py cwltool/command_line_tool.py cwltool/context.py cwltool/cuda.py cwltool/cwlrdf.py cwltool/cwlviewer.py cwltool/docker_id.py cwltool/docker.py cwltool/env_to_stdout.py cwltool/errors.py cwltool/executors.py cwltool/factory.py cwltool/flatten.py cwltool/__init__.py cwltool/job.py cwltool/load_tool.py cwltool/loghandler.py cwltool/__main__.py cwltool/main.py cwltool/mpi.py cwltool/mutation.py cwltool/pack.py cwltool/pathmapper.py cwltool/process.py cwltool/procgenerator.py cwltool/provenance_constants.py cwltool/provenance_profile.py cwltool/provenance.py cwltool/resolver.py cwltool/run_job.py cwltool/secrets.py cwltool/singularity.py cwltool/singularity_utils.py cwltool/software_requirements.py cwltool/stdfsaccess.py cwltool/subgraph.py cwltool/task_queue.py cwltool/udocker.py cwltool/update.py cwltool/utils.py cwltool/validate_js.py cwltool/workflow_job.py cwltool/workflow.py tests/__init__.py tests/test_anon_types.py tests/test_check.py tests/test_conditionals.py tests/test_content_type.py tests/test_context.py tests/test_cuda.py tests/test_cwl_version.py tests/test_default_path.py tests/test_dependencies.py tests/test_docker_info.py tests/test_docker_paths_with_colons.py tests/test_docker.py tests/test_empty_input.py tests/test_environment.py tests/test_examples.py tests/test_ext.py tests/test_fetch.py tests/test_http_input.py tests/test_input_deps.py tests/test_iwdr.py tests/test_js_sandbox.py tests/test_load_tool.py tests/test_make_template.py tests/test_misc_cli.py tests/test_mpi.py tests/test_override.py tests/test_pack.py tests/test_parallel.py tests/test_path_checks.py tests/test_pathmapper.py tests/test_procgenerator.py tests/test_provenance.py tests/test_rdfprint.py tests/test_recursive_validation.py tests/test_relocate.py tests/test_schemadef.py tests/test_secrets.py tests/test_singularity.py tests/test_singularity_versions.py tests/test_stdout_stderr_log_dir.py tests/test_streaming.py tests/test_subgraph.py tests/test_target.py tests/test_tmpdir.py tests/test_toolargparse.py tests/test_trs.py tests/test_udocker.py tests/test_validate_js.py tests/test_validate.py tests/test_windows_warning.py tests/util.py setup.py mypy-stubs
Fixing /home/kinow/Development/python/workspace/cwltool/mypy-stubs/prov/model.pyi
black --exclude cwltool/schemas setup.py cwltool.py cwltool tests mypy-stubs
reformatted mypy-stubs/prov/model.pyi

All done! ✨ 🍰 ✨
1 file reformatted, 412 files left unchanged.
flake8 cwltool/argparser.py cwltool/builder.py cwltool/checker.py cwltool/command_line_tool.py cwltool/context.py cwltool/cuda.py cwltool/cwlrdf.py cwltool/cwlviewer.py cwltool/docker_id.py cwltool/docker.py cwltool/env_to_stdout.py cwltool/errors.py cwltool/executors.py cwltool/factory.py cwltool/flatten.py cwltool/__init__.py cwltool/job.py cwltool/load_tool.py cwltool/loghandler.py cwltool/__main__.py cwltool/main.py cwltool/mpi.py cwltool/mutation.py cwltool/pack.py cwltool/pathmapper.py cwltool/process.py cwltool/procgenerator.py cwltool/provenance_constants.py cwltool/provenance_profile.py cwltool/provenance.py cwltool/resolver.py cwltool/run_job.py cwltool/secrets.py cwltool/singularity.py cwltool/singularity_utils.py cwltool/software_requirements.py cwltool/stdfsaccess.py cwltool/subgraph.py cwltool/task_queue.py cwltool/udocker.py cwltool/update.py cwltool/utils.py cwltool/validate_js.py cwltool/workflow_job.py cwltool/workflow.py tests/__init__.py tests/test_anon_types.py tests/test_check.py tests/test_conditionals.py tests/test_content_type.py tests/test_context.py tests/test_cuda.py tests/test_cwl_version.py tests/test_default_path.py tests/test_dependencies.py tests/test_docker_info.py tests/test_docker_paths_with_colons.py tests/test_docker.py tests/test_empty_input.py tests/test_environment.py tests/test_examples.py tests/test_ext.py tests/test_fetch.py tests/test_http_input.py tests/test_input_deps.py tests/test_iwdr.py tests/test_js_sandbox.py tests/test_load_tool.py tests/test_make_template.py tests/test_misc_cli.py tests/test_mpi.py tests/test_override.py tests/test_pack.py tests/test_parallel.py tests/test_path_checks.py tests/test_pathmapper.py tests/test_procgenerator.py tests/test_provenance.py tests/test_rdfprint.py tests/test_recursive_validation.py tests/test_relocate.py tests/test_schemadef.py tests/test_secrets.py tests/test_singularity.py tests/test_singularity_versions.py tests/test_stdout_stderr_log_dir.py tests/test_streaming.py tests/test_subgraph.py tests/test_target.py tests/test_tmpdir.py tests/test_toolargparse.py tests/test_trs.py tests/test_udocker.py tests/test_validate_js.py tests/test_validate.py tests/test_windows_warning.py tests/util.py setup.py
diff-quality --compare-branch=main --violations=pydocstyle --fail-under=100 pydocstyle_report.txt
-------------
Diff Quality
Quality Report: pydocstyle
Diff: main...HEAD, staged and unstaged changes
-------------
cwltool/run_job.py (100%)
-------------
Total:   1 line
Violations: 0 lines
% Quality: 100%
-------------
(venv) kinow@ranma:~/Development/python/workspace/cwltool$ echo $?
0

[kinow]

😄 ironically, whenever I type misspellings it's 50/50 I'll get it right

[kinow]

Alternatively we can create a file with one word per line, and use ignore-file=FILE_NAME.

[codecov]

Codecov Report

Merging #1715 (e97918a) into main (f3a35f3) will increase coverage by 0.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #1715      +/-   ##
==========================================
+ Coverage   66.43%   66.45%   +0.01%     
==========================================
  Files          89       89              
  Lines       15908    15908              
  Branches     4216     4216              
==========================================
+ Hits        10569    10571       +2     
+ Misses       4240     4238       -2     
  Partials     1099     1099              

Impacted Files	Coverage Δ
cwltool/job.py	80.27% <0.00%> (+0.39%)	⬆️

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