I think the reasoning is that

"Interpret the current user id from a cookie / kerberos authentication /
some key in the session"

and

"see whether the identified user exists in our system"

should be in different layers. I agree this leaves me scratching my head as
to when the distinction is useful. My first guess was 'the time between
deleting a user from the database and the expiration of an authentication
cookie', except I never delete users from my database, I would remove all
their group memberships instead.

I am used to systems that allow any username to be logged in but don't give
any useful permissions unless that user actually has an account. Think of
passing REMOTE_USER from a single sign on system, or a system that uses an
openid as the userid. The application will only know about a few of these
users but they will be logged in whether or not they exist in the
application's database.

While writing this example, perhaps this distinction could be used to offer
a 'create account' form to a user who had just presented a new openid? I'm
not entirely sure why that feature wouldn't just be a special group.

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