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Please download the package "xoops2.4.5-to-2.5.3.zip" again. It has been now updated.
The problem was that when I used the WinMerge, I zipped only the files that were different or missing. However, I forget that we recommended you to delete the "/modules/system" completely, i.e. as a result you were missing the files that didn't change in 2.5.x
I am sorry for it, and thank you for letting us know. The update package is now fixed, so if you download it now, you need only to copy the content of /modules/system/ to your installation.