Make a backup of the live wiki folder:

sudo cp /var/www/wiki <date>_wiki-backup -r
sudo chown mmclar <date>_wiki-backup/ -R
sudo tar -czvf <date>_wiki-backup.tgz <date>_wiki_backup

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

To fix styles, copy the default style from the backup folder to live folder

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