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I don't think this is meant to happen, but I don't know how to fix the problem. I also tried -Syu, but a same 'conflicting files' error occurs.
[root@... ...]# pacman -S pacman
resolving dependencies... done.
looking for inter-conflicts... done.
Targets: pacman-3.0.6-2
Total Package Size: 0.81 MB
Proceed with installation? [Y/n] y
checking package integrity... done.
cleaning up... done.
(1/1) checking for file conflicts [#####################] 100%
error: could not prepare transaction
error: failed to commit transaction (conflicting files)
pacman: /etc/pacman.d/core exists in filesystem
errors occurred, no packages were upgraded.
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Rename /etc/pacman.d/core in case you have reordered the servers and force the install:
# pacman -Sf pacman
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