tar zcpfv dokuwiki-backup.tar.gz /path/to/dokuwiki

This will create the dokuwiki-backup.tar.gz backup.

Read the changelog to see if there are any special things to consider

Download the newest release from the download site.

cd ~
wget http://.../dokuwiki-xxxx-xx-xx.tgz

tar zxvf dokuwiki-xxxx-xx-xx.tgz

Make sure to overwrite all files when prompted.

'cp' -af dokuwiki-xxxx-xx-xx/* /path/to/dokuwiki/

The quotes on cp assure that it will run as is, even if an alias is set.

Check copied files ownership and permissions (for details see permissions).

grep -Ev '^($|#)' data/deleted.files | xargs -n 1 rm -vf

Upgrade your template and plugins if necessary.

https://www.dokuwiki.org/install:upgrade

https://www.dokuwiki.org/install:unused_files