Applications lost permissions after flashing Marshmallow I upgraded my Nexus 5 from Android 6 preview 3 to the 6.0 final version by manualy flashing image files from google factory image.
All my applications lost permissions and crashing. I am unable to give permissions through settings too. The only solution I found so far is to reinstall applications. However I don't want to reinstall all of them for obvious reasons.

Please advise how to fix it.
For me the boot.img modification by Chainfire worked partially: device seems to be rooted (with supersu 2.51 beta), but twrp asks for password and cannot mount anything (I've posted a question about the latter). In particular I could not install supersu via adb sideload from recovery, as Chainfire recommends. Rather I just installed apk from system (using simple explorer).