This page has some documentation relating to setting up and using software, most of which is used on this website, which is hosted on Webfaction. This page is under development, and I will be adding to it over the coming weeks and months. Caveat Emptor - the information on this page should be taken with a grain of salt. I make no guarantees that it is 100% accurate and will take no responsibility if code listed here causes problems for you.
I found the best way to install dokuwiki on webfaction was to use a static application and install dokuwiki directly there using the dokuwiki installation instructions. When upgrading I installed dokuwiki freshly and carefully migrated my data files (meta, pages, attic) as well as ensuring that .htaccess in the root directory and acl.auth.php and users.auth.php in the conf directory were updated to reflect the old install's settings.
I found the best way to install Wordpress on webfaction was to use a static application and install wordpress directly there using subversion (instructions for installing Wordpress with subversion here. (For upgrading this should also work but I haven't tried it yet)