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You are right: altinstall shouldn't overwrite these
conflicting files. For idle and pydoc, I would think that
altinstall should install version-specific copies - users
actually might want to run an idle or pydoc associated with
a specific version, likewise for python-config. I'm
uncertain why smtpd.py is installed at all.

Would you be willing to work on a patch? You are right that
the shebang line should get updated during the installation,
too.