As of filesystem-2012.6-2 the folders /var/run and /var/lock will be replaced by symlinks to /run and /run/lock, respectively.
On most systems this is already the case, as initscripts create the symlinks on boot. However, these symlinks are not owned by any package, which is what we are fixing with this upgrade.
If the symlinks are already in place on your system (which should be the case for most people), then you can simply perform
# pacman -Syu --ignore filesystem && pacman -S filesystem --force
Otherwise, if /var/run or /var/lock are directories (e.g. if you are using systemd and never booted with initscripts) you need to delete the directories before performing the update. As these directories are used at runtime, it is recommended to shutdown any background tasks before performing
# rm -rf /var/run /var/lock && pacman -Syu && reboot
Note: In general, it is strongly advised to avoid the --force switch as it is not safe. However, in this particular case it is safe, and suggested to avoid having to manually delete the /var/run or /var/lock symlinks.
Lastly, on upgrading filesystem users of kernels prior to linux-libre-3.4 will get a warning about permissions on /sys. This is nothing to worry about, as of linux-libre-3.4 the permissions will be 555, and this upgrade reflects this in the filesystem package.