Searched before making this thread. Didn't see anything. Thanks in advance.
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An RUU is cleaner than an OTA; the latter only patches existing applications whereas the former installs them outright. Of course this is because an RUU also wipes your phone.
They also may be leftover files no longer used when you do an OTA, because it doesn't cleanup. If you do a hex compare of files and directories between the two methods, you will see differences.
I personally like to use RUU and get a clean start, especially when jumping from say JB to KK. I backup apps and setting with Titanium Backup first and restore later.
Though the guy above me is right. I wanted to make sure to point out what makes them different. An OTA is strictly an upgrade, where as an RUU contains the full software. And an RUU WILL erase everything on the device, whereas an OTA will not. Obviouslly for the case of those who do not root or anything like that an OTA is good enough. But for those that do root, and RUU may be the best way to upgrade the stock software. Hope made the differences clear, and I hope I didnt say anything redundant.
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