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How to update something using a patch (Wordpress, pmwiki etc.)

After unzipping, taring or whatever archive you used copy thepatch over the old files, replacing them.

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.
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