Hi Julian, while you argue that the error message is clear, and that this is not a bug, but a support request, I actually disagree with your assessment.
I think this _is_ a bug (and actually it has been filed here: #864640), because this behavior is not caused by a user having modified something themselves. It seems that this file might have been created by Synaptic, and later the user switching back to using apt on the command line gets this error, while apt itself does not require the existence of this file (please correct me if I'm wrong.) So this would actually be a bug in Synaptic or leftover code in apt that tries to access that file. (I am just guessing the part about the leftover code, so if you know more about that, let me know.) It seems to me that Debian currently lacks a way to install packages easily using a GUI. This means that people who are not super power users have no easy way to handle their packages. Older manuals will tell them to use Synaptic but then Synaptic is old and broken. This is why users will fall back to using apt on the command line. I find this overall situation a bit sad and I hope we could be a bit more helpful and empathic whenever such things happen and, if we have the time, try to refer the user to the information they are looking for. Cheers & thanks for your work on apt :) Ulrike