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This is more of a PSA for those coming across this issue in the future. I think people should do more of these.
I recently had problems installing packages where pacman told me several files already existed in the filesystem. This happened when I tried to install an individual official package, not a full system upgrade, so I couldn't find any relevant posts.
I tried to --force install the package, thereby rewriting all such files. But I noticed the next time I rebooted and logged into my system, my Cinnamon session would load extremely slowly (~2 mins) and I had several failed services.
Symptoms of the problem included:
- non-root partitions not mounted on boot
- users and groups added after initial system install were gone (including sudo)
- difficulty connecting to networks
- trying to start/restart services resulted in a Polkit-related error and a timeout
So after a while I found this post: https://bbs.archlinux.org/viewtopic.php?id=151915
It suggested that the polkit-related user and group were missing and I should check my /var/log/pacman.log around the time of my force installation, which I did. This revealed pacman overwrote several files in /etc including fstab, hosts, passwd, shadow and group.
Luckily pacman backed up all those files under the suffix *.pacorig so I by renaming the backups and rebooting I was thankfully able to return my system to normal.
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