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I was curious about one thing. I noticed that on the main menu bar, links such as that for Mailing List actually translate to http://www.drupal.org/mailing-list -- however, on my test drupal site, the link is something like www.domain.com/node/view/n (where n is the number of the node).
I use Apache 2.0.47. I've configured drupal to use cleaned URLs. With the rewrite-rules in .htaccess I got error-messages from my webserver (Bad Request). Maybe the rewrite-rules changed with Apache 2.0? I've had success with the following rules:
# Rewrite URLs of the form 'index.php?q=x':
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^/(.*)$ /index.php?q=$1 [L,QSA]