Rxpert83
Dr. Feelgood
It seems like we have a lot of people who are dependent on wugs toolkit to root their devices. Wugs toolkit is great, and I would highly suggest that people use it to root their device, but when you take an OTA you are normally unrooted. You then have 2 options. You can either use the any version in the wugs tookit, or just do it manually. Remember, Nexus devices are always rootable! Worry about whether you can root or not shouldn't be a reason not to take an OTA
Even if wugs is working fine, everyone should have a basic understanding of how to use fastboot. It'll save your rear some day.
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This looks long, buts its just the initial setup
If you aren't familiar with doing things from fastboot, chances are the first thing you are going to need to do is properly setup the folders to carry out the fastboot flash command. This setup is going to take the most time and after you have it all set up its very quick to do after that.
Setting up ADB:
1) Download the mini-SDK here and move it to something like C:\Android\platform-tools
our forums' mini-sdk
It contains:
adb.exe - Windows adb utility
fastboot.exe - Windows fastboot utility
fastboot-windows.exe - Windows fastboot utility
AdbWinApi.dll - adb link library for Windows
AdbWinUsbApi.dll - adb link library for Windows
2) Download your recovery & superuser files
I would highly suggest twrp. You can get it from here. As you may have guessed, you want the fastboot version
Su files:
For android 4.1-4.2.2:
https://dl.dropbox.com/u/63060876/Nexus 7/Root_Files.zip
It contains a busybox.zip, su.zip and permrecovery.zip unzip the folder you downloaded, but leave the 3 files inside of it zipped up
Su app For android 4.3+:
http://download.chainfire.eu/345/SuperSU/UPDATE-SuperSU-v1.51.zip
3) Put the recovery.img you just downloaded into your fastboot folder. For me it is in C:\Android\platform-tools. Also, transfer the 3 SU files you just downloded on the tablet.
To simplify things, I would also suggest renaming the long recovery name to recovery.img
4) Install recovery
a)Plug your tablet into your computer and reboot into bootloader/fastboot. If you dont know how to do this you hold power+volume up+volume down.
b)Once there, we need to open up a command prompt in the location where your sdk-tools are. If you are in windows 7 you can just shift+right click to select "open command prompt from here"
Or, you can navigate manually by using the command cd to change directory
c) Now that you are in fastboot and have the terminal in the right location, you just use the following command to install recovery.
***Note: if you did not rename the recovery, you'll have to type in the full name of the file instead of recovery.img
Congrats, you now how your custom recovery back. Reboot into it
5) Flash SU files
In recovery, flash the 3 SU files you've downloaded earlier.
To do this, select install, then navigate to where you placed the 3 files. Select the first file, then hit add more files to que, then add the 2nd and 3rd in the same manner. Then swipe to flash. after the install finishes, its a good idea to do the wipe dalvik cache and cache option, and then reboot into system
Reboot, done
Even if wugs is working fine, everyone should have a basic understanding of how to use fastboot. It'll save your rear some day.
---------------------------------------------------------------------------------------------
This looks long, buts its just the initial setup
If you aren't familiar with doing things from fastboot, chances are the first thing you are going to need to do is properly setup the folders to carry out the fastboot flash command. This setup is going to take the most time and after you have it all set up its very quick to do after that.
Setting up ADB:
1) Download the mini-SDK here and move it to something like C:\Android\platform-tools
our forums' mini-sdk
It contains:
adb.exe - Windows adb utility
fastboot.exe - Windows fastboot utility
fastboot-windows.exe - Windows fastboot utility
AdbWinApi.dll - adb link library for Windows
AdbWinUsbApi.dll - adb link library for Windows
2) Download your recovery & superuser files
I would highly suggest twrp. You can get it from here. As you may have guessed, you want the fastboot version

Su files:
For android 4.1-4.2.2:
https://dl.dropbox.com/u/63060876/Nexus 7/Root_Files.zip
It contains a busybox.zip, su.zip and permrecovery.zip unzip the folder you downloaded, but leave the 3 files inside of it zipped up
Su app For android 4.3+:
http://download.chainfire.eu/345/SuperSU/UPDATE-SuperSU-v1.51.zip
3) Put the recovery.img you just downloaded into your fastboot folder. For me it is in C:\Android\platform-tools. Also, transfer the 3 SU files you just downloded on the tablet.
To simplify things, I would also suggest renaming the long recovery name to recovery.img
4) Install recovery
a)Plug your tablet into your computer and reboot into bootloader/fastboot. If you dont know how to do this you hold power+volume up+volume down.
b)Once there, we need to open up a command prompt in the location where your sdk-tools are. If you are in windows 7 you can just shift+right click to select "open command prompt from here"

Or, you can navigate manually by using the command cd to change directory

c) Now that you are in fastboot and have the terminal in the right location, you just use the following command to install recovery.
Code:
fastboot flash recovery recovery.img
Congrats, you now how your custom recovery back. Reboot into it
5) Flash SU files
In recovery, flash the 3 SU files you've downloaded earlier.
To do this, select install, then navigate to where you placed the 3 files. Select the first file, then hit add more files to que, then add the 2nd and 3rd in the same manner. Then swipe to flash. after the install finishes, its a good idea to do the wipe dalvik cache and cache option, and then reboot into system
Reboot, done