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MacRumors was tipped off to another sighting of iPhone OS 4.0 in the wild. One iPhone developer noticed a single instance of the version 4.0 operating system being used. The new version was discovered via the developer's application analytics data.
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While these discoveries are by no means concrete proof, we have every reason to suspect that Apple is testing a new version of the iPhone (they've released a new model annually since its original debut), and new hardware would most certainly be accompanied by a new version of the OS. It's completely logical then that Apple would be prepping and testing new versions of the iPhone software.