I'm using Dreamhost's WordPress, Subversion, and Trac installations. My Subversion repositories are all in /repos/[projectname] and my Trac installations are all in /trac/[projectname]. I also have some other directories, such as /webapps/[appname] for web applications that I am working on. However, if I go to /trac/[projectname] in my browser, Wordpress serves up a 404 - which makes sense, there's no Wordpress page at that URL.
I wondered if this might be related to some plugins that I'm running. I'm going to start by disabling all of my plugins and turn them on one by one. However, I disabled them all (and even reset my theme to the default) and the same behavior was experienced.
I'm not sure if this is something I do programatically or through the administration console, and it really doesn't matter, but I didn't see anything in the console, so I'm guessing it's programatic (and that's why I'm asking here). I just need to identify directories that I don't want Wordpress to handle.
This is stock WordPress behaviour - its clean URLs work by redirecting all requests that don't match an existing file or directory to WordPress's index.php, which then handles based on the URL.
The following in your .htaccess prior to the WordPress RewriteRules should exclude those directories from this behaviour.
RewriteRule ^(trac|repos|webapps) - [L]