What every iPhone user should know is that, whenever you upgrade your jailbroken gadget to a new iOS, you will need to run the whole jailbreak process again. That being said, you will understand that all of your Cydia applications, as well as those which are built into iPhone applications, will be deleted permanently. Thus, you can never retrieve them after your upgrade. A good thing is, you can back your applications so that when the process is done, you can restore them from easily.
iPhone applications can easily be backed up using iTunes, but what about the Cydia Applications? No, these ones will NOT be taken care by iTunes.
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A few days ago, Tavis wrote a great article on