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Upgrading is not that hard.
- Backup - Copy files of the latest version - Run all patch files in the sql-directory. Starting from 125-0.0.1 to 0.0.2 till 0.0.6. After 0.0.6 you need to go to 0.6.1 up to 0.6.14
Or check the video's: http://www.cotonti.com/docs/en/videos/upgradevideos/
For the skin. I'm afraid you have to do a lot of copy paste.