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Check Perform build files cleanup option to enable build files cleanup.
Use Ensure clean checkout directory to ensure that the checkout directory corresponds to the sources in the repository at the build start. If detecting any modified or deleted files in the checkout directory before the build start Swabra will enforce clean checkout. The build will also fail if some newly created during previous build files can't be deleted.

Without Perform build files cleanup Ensure clean checkout directory you will only get warnings about modified and deleted files.