The buddy list is stored in the server's database.
It always gets retrieved from the server when you load up the game.
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Indeed, the installer and the updater often update files which should not be overwritten if they already exist. And if there are new features to be added (e.g. new sections in config files), those sections should be inserted.
After each update, I have once again to re-place all my GUI windows inside the application window, and exchange several skin files (because I prefer different font faces and sizes here and there...).