I run Dokuwiki on this website and when I get notices at the top of the page I always cringe. After my last update, I'm not sure why they intimidate me. Upgrading is very simple. Here are the steps I take.
Start in the directory above (..) where your wiki is.
cd /path/before/wiki
Make a backup copy of your wiki, just in case anything goes wrong.
cp -a ./wiki/ ./wiki-bak-xxxx-xx-xx
Download the latest version of Dokuwiki from Splitbrain with a command like the following command.
wget http://.../dokuwiki-xxxx-xx-xx.tgz
Extract it into a folder named dokuwiki-xxxx-xx-xx:
tar -xzvf dokuwiki-xxxx-xx-xx.tgz
Now copy/upload all its files over your old DokuWiki installation overwriting all existing files:
'cp' -rf dokuwiki-xxxx-xx-xx/{*,.??*} /path/to/wiki/
The quotes around cp ensures the command works even when cp is aliased to cp -i and the .??* ensures that hidden files are also copied.
See the Dokuwiki Upgrade docs for more details.