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I would expect the behavior of $PYTHONSTARTUP to be just
like typing the commands in at the interactive prompt,
except that the results of the individual expr_statements
are not printed.  That simply makes the old behavior
(__future__ directives ignored) a bug.  Instead of writing
documentation that is specific "this works, but this
doesn't", any remaining details of interpreter state that
differ between $PYTHONSTARTUP and entering commands at the
interactive prompt should be fixed.