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Allow setting allow_dirty=False in the config file #183

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This fixes a bug as was discussed and fixed in #180.

Symptoms: setting allow_dirty to False in the config file does not actually make it False.

florisla and others added 4 commits January 12, 2021 21:14
Currently, this one fails:
test_dirty_work_dir_with_allow_dirty_false_in_config_file_fails_with_warning
This test now passes:
test_dirty_work_dir_with_allow_dirty_false_in_config_file_fails_with_warning
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