Index: includes/bootstrap.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/bootstrap.inc,v
retrieving revision 1.366
diff -u -9 -p -r1.366 bootstrap.inc
--- includes/bootstrap.inc	24 Mar 2010 09:17:37 -0000	1.366
+++ includes/bootstrap.inc	25 Mar 2010 10:50:13 -0000
@@ -656,35 +656,32 @@ function drupal_settings_initialize() {
 function drupal_get_filename($type, $name, $filename = NULL) {
   // The location of files will not change during the request, so do not use
   // drupal_static().
   static $files = array();
 
   if (!isset($files[$type])) {
     $files[$type] = array();
   }
 
-  if (!empty($filename) && file_exists($filename)) {
+  if (!empty($filename)) {
     $files[$type][$name] = $filename;
   }
   elseif (isset($files[$type][$name])) {
     // nothing
   }
   // Verify that we have an active database connection, before querying
   // the database. This is required because this function is called both
   // before we have a database connection (i.e. during installation) and
   // when a database connection fails.
   else {
     try {
       if (function_exists('db_query')) {
-        $file = db_query("SELECT filename FROM {system} WHERE name = :name AND type = :type", array(':name' => $name, ':type' => $type))->fetchField();
-        if (file_exists($file)) {
-          $files[$type][$name] = $file;
-        }
+        $files[$type][$name] = db_query("SELECT filename FROM {system} WHERE name = :name AND type = :type", array(':name' => $name, ':type' => $type))->fetchField();
       }
     }
     catch (Exception $e) {
       // The database table may not exist because Drupal is not yet installed,
       // or the database might be down. We have a fallback for this case so we
       // hide the error completely.
     }
     // Fallback to searching the filesystem if the database could not find the
     // file or the file returned by the database is not found.
Index: includes/theme.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/theme.inc,v
retrieving revision 1.584
diff -u -9 -p -r1.584 theme.inc
--- includes/theme.inc	21 Mar 2010 04:05:23 -0000	1.584
+++ includes/theme.inc	25 Mar 2010 10:50:13 -0000
@@ -568,39 +568,35 @@ function list_themes($refresh = FALSE) {
   }
 
   if (empty($list)) {
     $list = array();
     $themes = array();
     // Extract from the database only when it is available.
     // Also check that the site is not in the middle of an install or update.
     if (!defined('MAINTENANCE_MODE') && db_is_active()) {
       foreach (system_list('theme') as $theme) {
-        if (file_exists($theme->filename)) {
-          $theme->info = unserialize($theme->info);
-          $themes[] = $theme;
-        }
+        $theme->info = unserialize($theme->info);
+        $themes[] = $theme;
       }
     }
     else {
       // Scan the installation when the database should not be read.
       $themes = _system_rebuild_theme_data();
     }
 
     foreach ($themes as $theme) {
       foreach ($theme->info['stylesheets'] as $media => $stylesheets) {
         foreach ($stylesheets as $stylesheet => $path) {
           $theme->stylesheets[$media][$stylesheet] = $path;
         }
       }
       foreach ($theme->info['scripts'] as $script => $path) {
-        if (file_exists($path)) {
-          $theme->scripts[$script] = $path;
-        }
+        $theme->scripts[$script] = $path;
       }
       if (isset($theme->info['engine'])) {
         $theme->engine = $theme->info['engine'];
       }
       if (isset($theme->info['base theme'])) {
         $theme->base_theme = $theme->info['base theme'];
       }
       // Status is normally retrieved from the database. Add zero values when
       // read from the installation directory to prevent notices.
Index: modules/system/system.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.module,v
retrieving revision 1.904
diff -u -9 -p -r1.904 system.module
--- modules/system/system.module	21 Mar 2010 21:20:43 -0000	1.904
+++ modules/system/system.module	25 Mar 2010 10:50:14 -0000
@@ -2251,18 +2251,19 @@ function _system_rebuild_module_data() {
  * @return
  *   Array of all available modules and their data.
  */
 function system_rebuild_module_data() {
   $modules = _system_rebuild_module_data();
   ksort($modules);
   system_get_files_database($modules, 'module');
   system_update_files_database($modules, 'module');
   $modules = _module_build_dependencies($modules);
+  system_list_reset();
   return $modules;
 }
 
 /**
  * Refresh bootstrap column in the system table.
  *
  * This is called internally by module_enable/disable() to flag modules that
  * implement hooks used during bootstrap, such as hook_boot(). These modules
  * are loaded earlier to invoke the hooks.
@@ -2423,18 +2424,19 @@ function _system_rebuild_theme_data() {
  *
  * @return
  *   Array of all available themes and their data.
  */
 function system_rebuild_theme_data() {
   $themes = _system_rebuild_theme_data();
   ksort($themes);
   system_get_files_database($themes, 'theme');
   system_update_files_database($themes, 'theme');
+  system_list_reset();
   return $themes;
 }
 
 /**
  * Find all the base themes for the specified theme.
  *
  * Themes can inherit templates and function implementations from earlier themes.
  *
  * @param $themes