I wish to know where the "Never ask again" checkbox boolean flag is stored and how to clear its value? Not necessarily programmatically, but manually - via setting, command or some tool. Tried clearing app data, uninstall, both uninstall and clear, tried manual switching the permissions on/off back and forth, tried even setting up a newer Marshmallow image for the emulator but no luck!
Both clearing data (Settings > Apps > your app > Storage > Clear Data) and uninstalling the app clear the status of this flag, along with clearing everything else related to runtime permissions for the app.
This behavior was tested on a Nexus 5 running Android 6.0, via this sample app.
I seem to recall seeing a manual option for this somewhere, but I can't find it now. It may be something that existed back in the M Developer Preview releases and got pulled for the final 6.0 release.