I just tried to pacman -Syu, where filesystem-2012.12-1 should be installed (also dbus would replace dbus-core and hwids would be installed, but this does not seem to have anything to do with the following problem).
However, the upgrade aborts with
error: failed to commit transaction (conflicting files) filesystem: /etc/arch-release exists in filesystem filesystem: /etc/mtab exists in filesystem filesystem: /etc/os-release exists in filesystem filesystem: /etc/profile.d/locale.sh exists in filesystem filesystem: /usr/lib/modprobe.d/usb-load-ehci-first.conf exists in filesystem filesystem: /usr/local/share/man exists in filesystem filesystem: /usr/share/man/man7/archlinux.7.gz exists in filesystem filesystem: /var/lock exists in filesystem filesystem: /var/mail exists in filesystem filesystem: /var/run exists in filesystem Errors occurred, no packages were upgraded.
I looked into the changes and I don't think this should happen. I certainly have not fiddled with those files manually.
When looking at the files listed above, I found out that all actual files are empty (zero size), while the links appear to be ok. However, neither files nor links belong to the package anymore (pacman -Qo reports "No package owns...").
I had the same problem (I think) last week, after I had upgraded the systemd package: The upgrade itself ran without error, but most (if not all) files of systemd were empty and no longer belonging to the package (thanks again to heftig, who guided me on the IRC to find that out). When I tried to reinstall systemd, pacman gave me a load of "foo exists in filesystem"-errors. The only way I saw to fix that was to --force the reinstall, and that worked.
However, I'm unsure if this was the best solution, and, more importantly, I'm wondering what the reason for this behaviour might be.
I don't know which of my configs (if any) would be helpful here, so I'll spare you those. I'll provide the details if required, of course.