Adding --allow-root to all wp-cli calls

wp-cli now requires --allow-root in order to run as the root user due to security concerns (see https://github.com/wp-cli/wp-cli/issues/982 and https://github.com/wp-cli/wp-cli/pull/973).  I've added this flag to all uses of wp-cli in provision.sh.  The auto-site setup stuff will need adjustment as well, but I'm less familiar with those and will have to take a closer look to see where that is needed.