We normally have 'Payload' folder as root once we unarchive IPA files. However, suddenly Xcode has started creating IPAs with 'Applications' folder as root. Hence MDM is failing to locate files.
Has anyone has faced a similar issue? We are running Xcode version 6.1.
Make sure the key "LSRequiresIPhoneOS" in the info.plist has the value "YES", and make sure the key has the correct case, i.e., IPhone versus Iphone. Earlier versions of Xcode were not as picky about that.