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The other advantage of splitting the entry points is that we can tweak Brett's plan to make the import machinery explicit such that it happens in a separate function that's only called from __init__.py.
That way the published hooks will always be from the on-disk implementation and never from the frozen one.
If you're after the ability to emit debugging messages in a way that doesn't cause fatal errors during system startup, the only way I can see is to have a "do nothing" module level display function in _bootstrap.py that is later replaced with a reference to builtins.print:
 def _debug(*args, **kwds):
 pass