The title pretty much says it all. What does "mount namespace separation" in the app SuperSU do and how does it affect other apps?
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From the man page for mount:
A mount namespace is the set of filesystem mounts that are visible to a process.
It makes it so that the superuser has separate mount points visible to it from the rest of the system/apps. I believe the intention is to prevent any issues when remounting partitions, such as remounting /system as read-write. With this option enabled it should remain read-only to unprivileged apps.
It can, however, just break things more. It made my SD card unusable in root apps: Internal and external SD storage inaccessible as root
Matthew Read
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+1. Using Systemless root, in my case, unchecking it works fine and resolved TiBu issues too – beeshyams Jan 06 '17 at 17:43