Copy the files in your newly extracted directory (pmwik-new/wordpress-patch) over the files of your existing software installation. For example, if your existing PmWiki/Wordpress installation is in a directory called pmwiki/wordpress, then one way to copy the new files over the existing ones is to enter the command:
cp -a pmwiki-new/. pmwiki
Note that BSD systems will not have the -a option as a command-line argument for cp, but that's okay, since it's just shorthand for cp -dpR, so use that instead of -a.
On (some) FreeBSD servers and Mac OS X systems you need to use
cp -Rpv pmwiki-new/. pmwiki
This works well on TxD shared hosting.