This affects your pc being able to communicate with your device after it reboots.
Most Nexus devices require you to put it in PTP Mode when the USB cable is plugged
in to communicate with your PC [and the Toolkit]. To do this you first install
drivers, then enable Developer options in settings [go to settings, About phone
and tap on Build number 7 times to enable the developer options screen], then go
to developer options and enable USB debugging. You then need authenticate your pc
from your device: make sure the usb cable is plugged in, pull down the top left
menu, select the USB mode option and change to either MTP or PTP mode. One of
these modes will bring a pop up on your device after a few seconds asking to
‘Allow USB debugging’. Select Always allow and then OK to do this.
This would normally need no further action on Android 5.1.1 and lower but with
Marshmallow [ANDROID 6] some devices, maybe all of them, THE DEVICE WILL REVERT
BACK TO CHARGING ONLY MODE WHEN THE DEVICE IS REBOOTED. Many of the Toolkit
routines reboot the device as part of its process so if the Toolkit reboots your
device and gets stuck on ‘waiting for usb debugging’ you just need to switch usb
mode back to PTP [or MTP depending which one worked] to continue.
This may change or there may be a setting to keep the device in whatever mode it
is set after a reboot, but it is important enough to make you aware snd will
hopefully stop people thinking there are problems with their device or the Toolkit.