Handle dirty local module repos by force checkout of commits and branches if needed #6219

Job	Run time
Get test file matrix	5s
setup (3.8, ubuntu-latest)	1s
setup (3.11, ubuntu-latest)	1s
setup (3.8, ubuntu-20.04)	1s
Run test_utils.py with Python 3.8 on ubuntu-20.04	1s
Run test_test_utils.py with Python 3.8 on ubuntu-20.04	1s
Run test_sync.py with Python 3.8 on ubuntu-20.04	1s
Run test_subworkflows.py with Python 3.8 on ubuntu-20.04	1s
Run test_schema.py with Python 3.8 on ubuntu-20.04	1s
Run test_refgenie.py with Python 3.8 on ubuntu-20.04	1s
Run test_params_file.py with Python 3.8 on ubuntu-20.04	1s
Run test_modules.py with Python 3.8 on ubuntu-20.04	6s
Run test_list.py with Python 3.8 on ubuntu-20.04	6s
Run test_lint_utils.py with Python 3.8 on ubuntu-20.04	11s
Run test_lint.py with Python 3.8 on ubuntu-20.04	12s
Run test_licenses.py with Python 3.8 on ubuntu-20.04	24s
Run test_launch.py with Python 3.8 on ubuntu-20.04	1m 14s
Run test_download.py with Python 3.8 on ubuntu-20.04	1m 35s
Run test_create_logo.py with Python 3.8 on ubuntu-20.04	1m 17s
Run test_create.py with Python 3.8 on ubuntu-20.04	1m 17s
Run test_components.py with Python 3.8 on ubuntu-20.04	2m 32s
Run test_cli.py with Python 3.8 on ubuntu-20.04	2m 8s
Run test_bump_version.py with Python 3.8 on ubuntu-20.04	2m 24s
coverage	1s
	13m 42s

Provide feedback