At this point the installer is not meant to be used to upgrade. As we make changes to the binaires, db, and quests I'll release smaller upgrade packs (and update the full installer with any changes) Those upgrade packs will only replace files changed by us, keeping your config files intact.
I fiddled with the idea of having 2.0 support an upgrade from 1.0, but really due to all the db changes made between 0.6.0 and 0.6.2 it really wasn't practical.
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