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Yes. I see the difference in the zip distribution created by tox, that README is present only if the Manifest is fixed. Also setup.py should be fixed.
I have no reason to learn about its replacement. I have no experience with upload to PyPI. I can not create the zip with install information, except automatically together with running tox test.
Is the manifest.in file left over from ez_setup ? or is still used somehow? if so it needs the reference to readme.md fixing.
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