I admit I didn't verify this since it is only used on Linux which wasn't the focus of my attention (but that's no excuse).
I updated the request but my understanding is that flake8/flake8 script could also be removed, then the whole line in MANIFEST.in could be removed as well. None of the entry point is using it and AFAIK, flake8/flake8 is not installed anywhere else.
Anyways, the focus of this issue was WIndows only and it is now fixed as far as I am concerned.
Marc Schlaich I did make it though. People using the recipe for a mercurial hook expect the relevant code to be in flake8/run.py. That said, to ease the pain of migration to flake8 2.0, I made the conscious decision to make flake8/run.py backwards compatible. I need to document, though, that it will be deprecated in some upcoming release of flake8 (probably 2.1 or 2.x).