pay particular attention to this reboot if you recently did "apt-get update" or similar to take care of the bash problem I don't understand. apt-get up

pay particular attention to this reboot if you recently did "apt-get update" or similar to take care of the bash problem I don't understand. apt-get update won't install new software on reboot. That just updates the index in apt. There's no other way to update bash without "apt-get update && apt-get install bash" and that won't impact anything on reboot. Your updated mysql config file sounds like you apt-get upgrade'd, installed a new version of mysql, or something like that and the changes didn't go into effect until the mysql process was restarted. I got bit in the ass with that same thing when I apt-get upgrade'd.