A while back someone complained of User DIrectories functioning in their virtual domains. I recently changed configuration so that they would not function in virtual domains without thinking about the ramifications on CGI scripts which this change broke,
In order to restore functionality to CGI scripts, I backed out this configuration change.
I do not remember who it was that originally wanted them removed, I can remove them from specific domains but it will break the ability to use CGI scripts from that domain (PHP and SSI will still work).
If you want them removed from your domain, with the understanding that CGI scripts will not work, then please send e-mail to email@example.com.