Scripts external to WordPress cause 404 errors

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My money would be on the .htaccess of your root directory is trying to route the /docuwiki request through WordPress, which is why it is failing.

Your .htaccess file should look something like this:

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>