I've been replaying the upgrade script and came across this:
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N: Ignoring file '50unattended-upgrades.ucf-old' in directory '/etc/apt/apt.conf.d/' as it has an invalid filename extension
This occurred at the end of the upgrade. The problem started right after this. I've checked my backup of /etc/apt/apt.conf.d and there is no such file in the backup.
Sorry I just remembered this. I totally forgot about it. I remember deleting the file but the error persisted, even after re-installing the apt package.
Still testing, but deleting the directory and re-installing from the backup seems to have fixed the problem (or so it seems at the moment). apt-get, apt-cache now works without throwing the error.
At this point, I think the problem may have been data corruption on /. This was a known issue with certain configuration, namely SSD, RAID0 and the 3.18 kernel (and others). See http://www.linuxquestions.org/questions ... 175543131/
for a discussion. I corrected the issue by dis-continuing the use of the 3.18 kernel from Jessie and installing a custom 4.3 (then a 4.5) kernel.
To make a pure Jessie system prior to the upgrade (as per the upgrade instructions), I switched to the 3.18 kernel and purged all of my custom kernels. I did not check whether the patch was applied to the 3.18 kernel in Jessie. I assume it would have been after this length of time.
Now to install the 4.9 kernel from Stretch and fsck the filesystems before going further,
I've updated my sig to point to the new link.