If you have ubuntu and they have a package for Planeshift (Arch Linux has at least a PKGBUILD) then you better wait for that. If you installed it manually with the normal installer, then you might uninstall it in order for the new installation to work properly. Maybe this is done automatically with the new installation or not.
What I heard about, is that all player logs, infos etc. are saved in the /home directory now and I guess also in different manner. So there is no real need to save all the config files, but in any case it is good to have your chat log and your questlog somewhere. Even if it will be different now, you can look anything up manually in the old files.
PS:
I kind of skipped through history.txt and history2007.txt quite interesting.