My understanding is that you cannot update base WP from earlier versions to the current one from the appliance itself. You need to do a new build using tkldev appliance instead. Follow the tkldev appliance docs to do that. Once you install the appliance in a VM you will see a code in wordpress/conf.d/downloads:

#!/bin/bash -ex

dl() {
    [ "$FAB_HTTP_PROXY" ] && PROXY="--proxy $FAB_HTTP_PROXY"
    cd $2; curl -L -f -O $PROXY $1; cd -
}

SRC="/usr/local/src"
PLUGINS_SRC="/usr/local/src/wp-plugins"

# wordpress installation
dl http://wordpress.org/latest.tar.gz $SRC

Besides that, you will be able to remove or add plugins at your own will.

regards,

Lin Pro

However; for the record the TurnKey appliance should support updating the WordPress software from within a running WordPress appliance. Unfortunately though it seems that the permissions aren't quite right to support that...

For any seeking the workaround, please see the TurnKey Issue Tracker.