=== modified file 'includes/bootstrap.inc'
--- includes/bootstrap.inc	2009-07-01 12:47:30 +0000
+++ includes/bootstrap.inc	2009-07-13 06:52:15 +0000
@@ -391,9 +391,9 @@
 }
 
 /**
- * Initialize variables needed for the rest of the execution.
+ * Initialize PHP environment.
  */
-function drupal_initialize_variables() {
+function drupal_initialize_php() {
   if (!isset($_SERVER['HTTP_REFERER'])) {
     $_SERVER['HTTP_REFERER'] = '';
   }
@@ -454,7 +454,7 @@
  * Loads the configuration and sets the base URL, cookie domain, and
  * session name correctly.
  */
-function conf_init() {
+function drupal_initialize_settings() {
   global $base_url, $base_path, $base_root;
 
   // Export the following settings.php variables to the global namespace
@@ -605,7 +605,7 @@
  * with variable_set() as well as those explicitly specified in the configuration
  * file.
  */
-function variable_init($conf = array()) {
+function variable_initialize($conf = array()) {
   // NOTE: caching the variables improves performance by 20% when serving cached pages.
   if ($cached = cache_get('variables', 'cache')) {
     $variables = $cached->data;
@@ -1322,11 +1322,11 @@
   switch ($phase) {
 
     case DRUPAL_BOOTSTRAP_CONFIGURATION:
-      drupal_initialize_variables();
+      drupal_initialize_php();
       // Start a page timer:
       timer_start('page');
-      // Initialize the configuration
-      conf_init();
+      // Initialize the configuration, including variables from settings.php.
+      drupal_initialize_settings();
       break;
 
     case DRUPAL_BOOTSTRAP_EARLY_PAGE_CACHE:
@@ -1366,8 +1366,8 @@
       break;
 
     case DRUPAL_BOOTSTRAP_VARIABLES:
-      // Initialize configuration variables, using values from settings.php if available.
-      $conf = variable_init(isset($conf) ? $conf : array());
+      // Load variables from the database, but do not overwrite variables set in settings.php.
+      $conf = variable_initialize(isset($conf) ? $conf : array());
       break;
 
     case DRUPAL_BOOTSTRAP_LATE_PAGE_CACHE: