Now it seems like you may have re-written system files with nitdroid folders...

The easiest method would be to do a rootfs flash which would mean your ~/MyDocs/ partition wouldn't be affected but other data like logs, messages, apps etc would be erased...

You can read this guide to do a simple rootfs-only flash...

If you have important data or want to try to fix this issue by accessing your file system you may want to follow FIX MALF STATE steps till step 7 and once your device is mounted on your Linux/MAC system you can do whatever you want to it...