So, I've just updated to the latest Pure Nexus - did a wipe and clean install - and I'm trying to get my apps set up again, but I can't grant permissions through system settings. If an app actually pops up and requests a permission, I can allow it; but for some apps, this doesn't happen. Home Remote Control, for example, won't request the storage permission it needs to access my ssh key. So I go into settings->apps, find the app, tap permissions, try to enable the storage permission, and..."screen overlay detected". Except there is no screen overlay active. I have disabled every app's "draw over other apps" permission. I even found the "show system" option in the list and disabled all system apps' ability to draw over other apps. At this point, SYSTEMUI can't draw over anything else! And I'm still getting "screen overlay detected" when I try to change permissions. Any advice? Is there another way to manage permissions in Marshmallow (like maybe an xposed module)?
EDIT: Thought I should also mention, the issue persists in Safe Mode.