Application File Problems

All my Applications (which were names of the files inside eg. iFish) changed to the iTunes style of code (eg. A4FEF8AF-DEDD-493A-A43A-5EED94C2D2FB)

may have something to do with the chmod commands i used for the applications

Sorry, I do not know iPhone or iPod or whatever you are using. You should ask on specialized forum.