I've come across it as I'm creating a Debian package of the Python package in the same tree — I'm happy to be told this is a Bad Idea and that they should be in different places.

The broken symlinks are relative and in debian/tmp, and will point to locations provided by other Debian packages once my package is installed in the right location.

FWIW, I'm getting round it at the moment by walking the directory tree and removing the files is os.path.islink(filename) and not os.path.exists(os.path.join(filename, os.readlink(filename))).

I'm happy to provide tests and a patch if necessary.