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i have proformed the upgrade once safely. when i proformed the upgrade the second time on another XOOPS install i forgot to turn on the php debug on and i pressed the the button more than 1 on the XOOPS update page.
if you upload all the files correctly set the permissions and make sure the php debug is on before you start the upgrade it should work. when you load the xoopsupdate for the first time don't do anything but hit the refresh button after that page loads then press the update button 1 time only after that update all of your modules. that is how the succssfull update is done. if you don't follow the directions or are asleep while upgrading a site you will screw up badly. i have to now download and install a 2.0.13 to get the users and groups and other stuff working so basically i have to redo the site from ground up taking stuff from an old database to a new one without causing downtime. hopefully i can do it safely. just have everything backed up and do the things you try on a non production site. i will post my findings after i finish if i get it working.