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If you follow the instructions and flash the RUU successfully before setting S-ON, which I highly recommend or you will brick your phone, you will have the stock hboot and recovery installed by the time you get to step for the set S-ON.are you suppose to do this with a certain recovery?
a little warning from my experience, do NOT do the "fastboot oem writesecureflag 3" until you flash the RUU or you WILL brick your phone. took me like 8 hours just to unbrick mine