If you're using a Unix based system such as OSX (there's probably a similar methoud under Windows as well), you can pretty easily write a shell script that will "touch" your apps in any order you specify. When it "touches" them, it automatically updates their modification date, so if you "touch" the items that you want at the bottom of the list first, and the items that you want at the top of the list last, that should sort it out for you.
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