Make a backup of the /var/www/html/wiki/lib/tpl/default folder (or the entire /var/www/wiki folder):

sudo cp /var/www/wiki <date>_wiki-backup -r sudo chown mmclar <date>_wiki-backup/ -R

Use upgrade extensions in wiki, or follow directions for upgrading manually

To fix styles, copy from the backup /lib/tpl/default folder to /var/www/wiki/lib/tpl/default

sudo cp <date>_wiki-backup/lib/tpl/default/ /var/www/wiki/lib/tpl/ -r

Archive the backed up folder sudo tar -czvf <date>_wiki-backup.tgz <date>_wiki_backup