TWRP patching /system I recently flashed a stock system image to take an OTA update and have only booted to TWRP since. (I didn't flash it) I did root, though. 
When I was browsing /system I found that reboot-from-recovery.p was renamed to reboot-from-recovery.bak 
My question is was this done by SuperSU or TWRP? and could this be the only modification?

Thanks.
It's done by TWRP.

If you're rooted, SuperSU modifies /system as well to put files there to give you root.