[SuperSU] Chainfire:
[MENTION=535343]all[/MENTION]

First, on Android 6.0, some devices cannot remount /system read/write in Android (only in Recovery). This is why modifications to /system may fail, such as build.prop edits, bloat removal, etc. I'm not quite sure yet why or how this happens. The only known workaround at this time is changing fstab to mount /system rw, but this would negate the advantages of not touching /system.

Second, yes, some apps look for the su binary in hardcoded locations. SuperSU in systemless mode by default does not touch /system, but if you create /system/bin/su and/or /system/xbin/su yourself (with the above statement in mind, doing so from Recovery is probably best), it will override those files with the correct binary each boot. This should fix most misbehaving apps (that do not rely on modifying /system on a device which currently does not allow this).

Both of these issues have several ways of working around them, and if/when we get unionfs/overlayfs working, it will solve both problems in one go.

Lastly, the "enable superuser" option is grayed out (but ticked) because you currently cannot temporarily disable su like you can with a /system install. It is already enabled.

It shouldn't. But I can see it happening on rare occasions.

Not yet, but soon I will.

And yes, you probably modified /system by now.

Nice catch, I will update the patcher to skip symlinks. Let me know next update if it worked please. Thanks for your in-depth investigations and actually helping fix stuff :)

Please post your stock boot.img, and if possible also the auto-patched one.

Yes, you can just flash stock before flashing SuperSU. Though if you did so before, in most cases it should still have a backup so you do not need re-flash back to stock boot image first. Encryption is switched from forced to optional in the boot image modifications, yes.

Try reflashing stock boot image (and or cataclysm) then reflashing the SuperSU ZIP.

See the comment at the top of this post. Alternatively, there is a switch in the installer script to disable systemless installs and do a system install instead, but there's currently no way to set it if run from TWRP.

Not sure what's going on, perhaps you're having the same issue as [MENTION=1162986]Captain_Throwback[/MENTION] ?

Post a logcat created immediately after boot.

You will keep getting this notice until TWRP is updated.

Headshaking confirmed! :)

Something like that should indeed do the trick.

Reflash stock /system.

Are you saying the camera also doesn't work with the 2.61 root?

You probably need to modify it from recovery because /system isn't currently writable (see my comment at the top of this post).

Baby don't hurt me...

CF-Auto-Root will be updated as soon as this is a little more stable.

Unless the new kernel is updated with the required patches for SuperSU, you'd need to reflash the SuperSU ZIP after flashing the custom kernel.

It only works on Lollipop on Samsung 5.1.

Interesting. Unfortunately the /tmp/recovery.log won't help, its the logcat from the short boot (that automatically reboots) after install that we really need, and you can't get that. Maybe a logcat from the freshly booted system may help.

See my comments at the top of this post.

Reactivation lock is not compatible with modified boot images. They are mutually exclusive.