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I've been getting the "there was internal api error" message in Xcode and I've finally figured out what the problem was. Apps run with the same bundle identifier will result in this error.
Turns out that the apps aren't being deleted in Organizer. When I delete them, they disappear. But when I quit Xcode, reopen, enter organizer, the applications are still there.
Are these Applications stored in Xcode or on my iDevice? Can I go in and manually remove them? What directory?
Has anyone had this problem? Solutions?