I never would have thought that zipped files would have been inside other zipped files. I got through most of them, but appear to be stuck on fastboot reboot-bootloader.
When I finished the previous command, fastboot -w update image-mysid-icl53f.zip, the phone restarted and showed the set up screen. I then put in fastboot reboot bootloader, it said waiting for device, and the screen went dark. Nothing has happened since. If I hit the power button, the first welcome screen is there. (interestingly, the power button worked that time.)
So... I never got to run fastboot reboot-bootloader or fastboot oem lock.
I assume I need to do these to finish the process, but it hasn't moved from waiting for device.
Well, I haven't run this process (no need to blessedly, happily GNex rooted), and I think you should wait for advice from Yeahha or other more experienced than I, but it looks to me as if either you somehow rebooted the device after flashing the new image, or there may be an error/omission in the instructions, which read
fastboot -w update image-mysid-icl53f.zip
fastboot reboot-bootloader
fastboot oem lock
the fastboot -w command erases the user data and cache and the "update image-mysid-icl53f.zip" part reflashes the device with the stock image. The fact that after you did fastboot -w update image-mysid-icl53f.zip it restarted to the startup screen suggests it now has left bootloader (fastboot) mode and is fully booted as a virgin GNex so to speak. In that case of course the next command, fastboot reboot-bootloader, will not work because the device is not in bootloader mode. What I would do now (but wait for others to confirm) would be to power off the device, open a new command line and navigate again to your Gnex folder, turn the device on in bootloader mode (hold both vol up and vol down buttons in at same time and press power button), and it should boot into bootloader. Then do
fastboot devices
to be sure you are connected, and if so do
fastboot oem lock
and you should be done.
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