Just some further info for anyone who may come across this in the
future, this happened to me a few more times. After the third time it
happened I was hitting my head against the wall and finally noticed a
simple error in a signal handler I was importing into models.py. After
fixing that bug the configuration error went away and I was able to
continue developing the site. So when I said in the second post that I
changed something minor unrelated to the issue, I probably fixed a bug
that was crashing the authentication middleware.

So I believe the issue is:
    The middleware files are processed in order
    The authentication middleware needs models and so models.py is
imported
    The import of models.py fails
    The authentication middleware fails to load models properly and so
it fails
    The remote user middleware checks for the authentication
middleware which is not properly loaded
    It throws the error with message 'remote user middleware needs
authentication middleware...' masking the actual cause of the issue

I am just guessing, I haven't looked at much of the Django internals,
but I am hoping that my experience will be helpful for someone else.

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