Hi
@Chainfire,
Thanks for such a fantastic method for doing this!
I also just tried the Nexus 5 (hammerhead) CF-AutoRoot after reflashing with the 6.0.0 factory image released yesterday. Booting CF-AutoRoot (the version for Android 5.0 on your site) went fine, the whole thing ran as per usual without any apparent errors, but when the phone rebooted it got stuck on the booting animation (four animating coloured circles). At this point adb still worked so I could get a shell on the device, but I'm not really sure what to look for - the su binaries were in the expected locations and running them did nothing (they just exited immediately returning 1) which I assumed was because the boot process was still active.
Note that I did all this *after* booting the device with 6.0.0 for the first time, so it wasn't the app cache being rebuilt - that did indeed take a while, but finished successfully before I ran CF-AutoRoot.
In the end I just reflashed the system partition and everything went back to normal and the phone finished booting, but of course without SuperSU installed.
If there's anything I can do to help test or work out what happened, let me know. I'm also happy to beta test any changes if you don't have access to a Nexus 5. You've asked for a recovery image for unsupported devices, so
here's the one for Nexus 5 / hammerhead for Android 6.0.0 (9.8MB) in case that helps. But like I say, the install process ran with no errors I could see, so perhaps that won't be so helpful.
Thanks again for your amazing efforts!