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Hi,
Well, my XOOPS website has only been up for 5 days, but I have used most of the functions in admin, added links, changed templates, themes, done a fair bit with config. changes, and added various blocks of code (html wrapped in the necessary PHP code), changed meus, added menu blocks in manually.
So, as far as I know, this all works fine. The 644 is default permission on most servers, and even the previous hosts I was with, I used 644's for any PHP applications, osCommerce, Drupal, Mambo, phpwebsite and a few others.
Most FTP clients let you select all the files in a path, and then you can do a mass permissions change. If you are concerned, possibly try and change all the files that reside ina particular module first, try that module, and then if that works without errors, continue to change/test other paths.
Peter