Gettting Rid of "cgi-system" When Upgrading Drupal on Dreamhost

I recently upgraded this site from Drupal 5.1 to 5.7 on Dreamhost and ran into an odd problem. After upgrading, all of my urls included the path cgi-system. So, instead of my login page being at juliakm.com/user, it was at juliakm.com/cgi-system/user. Because of the url issue, my site lost its theme.

To solve the problem, I had to add a $base_url setting in my settings.php file in sites/default to http://www.juliakm.com. However, because I had used Dreamhost's 1-click install, it was impossible to edit this file via FTP. Instead, I had to log into my site via SSH, and then chmod the permissions on settings.php to make the file editable.

First, I navigated to the right folder:

cd mysite.com/sites/default

Next, I changed the settings.php permissions:

chmod 755 settings.php

Finally, with pico, I was able to uncomment the $base_url line and edit it:

$base_url = 'http://www.juliakm.com';  // NO trailing slash!

It looks like I am not the only one who has ran into this problem on Dreamhost. Here are other tales of Drupal + Dreamhost upgrade misery:
http://drupal.org/node/60139
http://drupal.org/node/163085
http://drupal.org/node/163870