Updated for NAE. When the NAE tar.md5 comes out you can just flash it directly rather than doing all this.
This will update everything (firmware, modem, bootloader, ROM, recovery, etc) to NAE. As long as you're coming from stock or mostly stock, this should work, and you will still have all your data and apps. It will also probably work coming from another MF9, MJA, or MK2 based ROM, but you may have problems (in which case you can just wipe data. The whole process should take less than 30 minutes, not counting the time it takes to download the stock tar.md5 image. I recommend starting it now (link in Step 2) so it will be ready when you need it. This will NOT work if you've already tried to take the NAE OTA and it failed because you weren't fully stock.
You will need odin. It can be downloaded from this thread. Alternatively, if you're using OS X or Linux, I found that Heimdall works very well in place of odin. There are a few extra steps involved though, but if you install Heimdall Frontend then you don't have to mess with the terminal.
Step 1: Backup your current ROM with TWRP, CWM, or Philz.
Step 2: Download the MK2 tar.md5 from sammobile. Sammobile is pretty slow to download, but I found a mirror and a second mirror. I also made a torrent that might be faster (please seed if you use it to speed it up for everyone). Flashing this with odin does NOT wipe data. You can verify it by opening it in an a program that supports tar and looking at the files within it; those are the partitions it overwrites. This will give you stock MK2 recovery, bootloader, modem, firmware, and software.
Step 3: Use odin to flash it over your current ROM. To do this, you need to first put the phone into download mode. Power it off completely, then press and hold volume down, home, and power. Then connect it to your computer.
In odin, I just left default odin settings checked. Make sure that you add the tar.md5 in the PDA slot and apply it. Reboot and verify that your data is all there. You can still easily revert to the backup you made in Step 1 if things aren't right.
Step 4: Put the MK2 to NAE OTA on your external sd card (not internal). You don't need to rename it.
Power the phone off completely. Then press and hold home, volume up, and power to get into stock recovery. Navigate to where you put the OTA zip on your external sd card and flash it. It will reboot a couple times during the update, including one time where it seems like it's booted up and done before it powers off again. You'll know it's done when you get a popup notification saying it completed successfully. All your data and apps should still be there.
Note: From this point on, performing any of these steps will set the Knox flag. So if you just purchased the phone (within your return window) or are having issues and may need a replacement, you may want hold off on root. Sprint may or may not check for this during a warranty replacement. Insurance replacements should be fine.
Step 5: Go back into download mode and flash CF Auto Root through odin. You should now have root, and knox will not complain. You'll need to re-download the SuperSU app from the Play Store though. Open the app and let it update the su binary to the newest version.
Step 6: Flash TWRP (or CWM or Philz) through odin (it didn't work for me with goo manager). Optionally reboot into recovery to make sure it actually stuck.
This will update everything (firmware, modem, bootloader, ROM, recovery, etc) to NAE. As long as you're coming from stock or mostly stock, this should work, and you will still have all your data and apps. It will also probably work coming from another MF9, MJA, or MK2 based ROM, but you may have problems (in which case you can just wipe data. The whole process should take less than 30 minutes, not counting the time it takes to download the stock tar.md5 image. I recommend starting it now (link in Step 2) so it will be ready when you need it. This will NOT work if you've already tried to take the NAE OTA and it failed because you weren't fully stock.
You will need odin. It can be downloaded from this thread. Alternatively, if you're using OS X or Linux, I found that Heimdall works very well in place of odin. There are a few extra steps involved though, but if you install Heimdall Frontend then you don't have to mess with the terminal.
Step 1: Backup your current ROM with TWRP, CWM, or Philz.
Step 2: Download the MK2 tar.md5 from sammobile. Sammobile is pretty slow to download, but I found a mirror and a second mirror. I also made a torrent that might be faster (please seed if you use it to speed it up for everyone). Flashing this with odin does NOT wipe data. You can verify it by opening it in an a program that supports tar and looking at the files within it; those are the partitions it overwrites. This will give you stock MK2 recovery, bootloader, modem, firmware, and software.
Step 3: Use odin to flash it over your current ROM. To do this, you need to first put the phone into download mode. Power it off completely, then press and hold volume down, home, and power. Then connect it to your computer.
In odin, I just left default odin settings checked. Make sure that you add the tar.md5 in the PDA slot and apply it. Reboot and verify that your data is all there. You can still easily revert to the backup you made in Step 1 if things aren't right.
Step 4: Put the MK2 to NAE OTA on your external sd card (not internal). You don't need to rename it.
Power the phone off completely. Then press and hold home, volume up, and power to get into stock recovery. Navigate to where you put the OTA zip on your external sd card and flash it. It will reboot a couple times during the update, including one time where it seems like it's booted up and done before it powers off again. You'll know it's done when you get a popup notification saying it completed successfully. All your data and apps should still be there.
Note: From this point on, performing any of these steps will set the Knox flag. So if you just purchased the phone (within your return window) or are having issues and may need a replacement, you may want hold off on root. Sprint may or may not check for this during a warranty replacement. Insurance replacements should be fine.
Step 5: Go back into download mode and flash CF Auto Root through odin. You should now have root, and knox will not complain. You'll need to re-download the SuperSU app from the Play Store though. Open the app and let it update the su binary to the newest version.
Step 6: Flash TWRP (or CWM or Philz) through odin (it didn't work for me with goo manager). Optionally reboot into recovery to make sure it actually stuck.
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