After having some problems with Drupal's File System and Caching settings (http://drupal.org/node/513054), I found that the variables were being overridden by the $conf array in settings.php that is created when making a new site in Aegir. After digging, I found that the Provision module creates a site's settings.php in _provision_drupal_create_settings_file().
I noticed that this function is hardcoded to take in the contents of provision_drupal_settings.tpl.php to create settings.php, and had a few questions about this.
1) Why is the $conf array set in settings.php? Why not leave control of these Drupal settings to the database?
2) What is the best method for removing the $conf array? I figure I could just delete it from the settings.php file for any site I want to change the values of, but worry that it'll be regenerated when I migrate a site. Another solution would be to edit it out of provision_drupal_settings.tpl.php, but I'd rather not edit a core Aegir/Drush/Provision file if a better way exists. Is there a mechanism for providing an alternative template?
Thanks!