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Something that tripped us up (but seems right) early on was that mbt ensures that your git checkout is clean (including untracked files) before each module build. I'm inferring then that it expects any artifacts to be stored outside the git checkout, and/or their paths included in a .gitignore file.
Build is free to produce the artifacts inside repo during the build. However, if artifact path is not in .gitignore, next time you run mbt the dirty workspace check will kick-in.
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