Step 1 - Collect Needed Files:

Step 2 - Flash Stock System Image:

Code: adb reboot bootloader

Code: fastboot erase system fastboot flash system system.img

Step 3 - Flash Update Image:

Code: adb sideload 2bef78c4a5ec8dbaa3df9d94e78af8622cd2a394.signed-shamu-LVY48F-from-LVY48E.2bef78c4.zip

I had a hard time finding this information, so thought I would post a new thread!After you root your phone, even if using standard recovery, the OTA updates will no longer install. You may get the notifications, but after it reboots to install, you will get a failed notification. Even if you uninstall root. This is because if there is any change to the system image at all, the OTA update will fail.To install it is actually easy, just requires some legwork. I assume you understand what the bootloader is, and what adb and fastboot tools are since your phone is already rooted. If you used a toolkit, there are plenty of guides on XDA on how to install these tools manually.Visit the Google System Images page and download the image for your existing ROM. Check your About Device page to get the exact ID, it should say something like LVY48E.Extract the system.img file so you can flash it later.Download the OTA image. All OTA images are listed on the Nexus 6 OTA Images thread. Find the file which upgrades "From" your current ROM id.It will be named something like, and this file in particular flashes to the new LVY48F version from LVY48E version.This step replaces your system image with the stock system image. This will not delete your apps or other personal data, only the information stored on the system partition. The only exception is if you rooted and stored any data on this partition. Plug your phone into your computer. There is no way to do this without a PC.Reboot into bootloader mode either from booting with POWER+VOLDOWN or via adb:and flash the imageAt this point your system is stock again (unrooted).Enter the recovery mode. You can also do this via TWRP but I will cover with stock recovery. Pressuntil you see RECOVERY and pressto choose. You are now in recovery.Press and holdand taponce to get the recovery menu. Then useto select "apply update from ADB" and thento selectI had to unplug and plug my phone back in at this point to get it to show up to adb. You can confirm it is visible with the commandApply the OTA update file using the following command, replacing the file name with your own:After a few minutes the sideload will complete, the phone will reboot and optimize apps, and you can verify the update worked by checking your about system page again.To root your device again, re-install SuperSU and you're good to go.