diff --git includes/common.inc includes/common.inc
index ffa802d..fc0015b 100644
--- includes/common.inc
+++ includes/common.inc
@@ -2878,12 +2878,6 @@ function drupal_aggregate_css(&$css_groups) {
   $directory = file_directory_path('public');
   $is_writable = is_dir($directory) && is_writable($directory);
 
-  // For non-aggregated files, a dummy query string is added to the URL when
-  // rendering the HTML tag (see drupal_pre_render_styles()). For aggregated
-  // files, it is instead added to the data from which an md5 hash is generated,
-  // so that a changed query string triggers a new aggregate file to be created.
-  $query_string = '?' . substr(variable_get('css_js_query_string', '0'), 0, 1);
-
   // For each group that needs aggregation, aggregate its items.
   foreach ($css_groups as $key => $group) {
     switch ($group['type']) {
@@ -2893,7 +2887,7 @@ function drupal_aggregate_css(&$css_groups) {
         if ($group['preprocess'] && $preprocess_css && $is_writable) {
           // Prefix filename to prevent blocking by firewalls which reject files
           // starting with "ad*".
-          $filename = 'css_' . md5(serialize($group['items']) . $query_string) . '.css';
+          $filename = 'css_' . md5(serialize($group['items'])) . '.css';
           $css_groups[$key]['data'] = drupal_build_css_cache($group['items'], $filename);
         }
         break;
@@ -2982,7 +2976,7 @@ function drupal_pre_render_styles($elements) {
   // browser-caching. The string changes on every update or full cache
   // flush, forcing browsers to load a new copy of the files, as the
   // URL changed.
-  $query_string = '?' . substr(variable_get('css_js_query_string', '0'), 0, 1);
+  $query_string = '?' . substr(variable_get('css_js_query_string', '0'), 0, 2);
 
   // Defaults for LINK and STYLE elements.
   $link_element_defaults = array(
@@ -3020,10 +3014,7 @@ function drupal_pre_render_styles($elements) {
         // for the aggregate file.
         if (isset($group['data'])) {
           $element = $link_element_defaults;
-          // The aggregate file name already incorporates the dummy query
-          // string information. The query string does not need to be added to
-          // the URL.
-          $element['#attributes']['href'] = file_create_url($group['data']);
+          $element['#attributes']['href'] = file_create_url($group['data']) . $query_string;
           $element['#attributes']['media'] = $group['media'];
           $element['#browsers'] = $group['browsers'];
           $elements[] = $element;
@@ -3475,6 +3466,10 @@ function drupal_region_class($region) {
  *       Aggregate the JavaScript if the JavaScript optimization setting has
  *       been toggled in admin/config/development/performance. Note that
  *       JavaScript of type 'external' is not aggregated. Defaults to TRUE.
+ *   - version
+ *       If not empty, the version is added as a query string insead of the
+ *       incremental query string that changes on cache clearing. Primarily
+ *       used for libraries.
  * @return
  *   The constructed array of JavaScript files.
  * @see drupal_get_js()
@@ -3516,11 +3511,14 @@ function drupal_add_js($data = NULL, $options = NULL) {
         'misc/drupal.js' => array(
           'data' => 'misc/drupal.js',
           'type' => 'file',
+          'preprocess' => FALSE,
+          // This version should be incremented whenever drupal.js changes.
+          // It will not match the core version number.
+          'version' => '7.0',
           'scope' => 'header',
           'weight' => JS_LIBRARY - 1,
           'cache' => TRUE,
           'defer' => FALSE,
-          'preprocess' => TRUE,
         ),
       );
       // Register all required libraries.
@@ -3564,6 +3562,7 @@ function drupal_js_defaults($data = NULL) {
     'cache' => TRUE,
     'defer' => FALSE,
     'preprocess' => TRUE,
+    'version' => NULL,
     'data' => $data,
   );
 }
@@ -3615,8 +3614,10 @@ function drupal_get_js($scope = 'header', $javascript = NULL) {
   }
 
   $output = '';
-  $preprocessed = '';
-  $no_preprocess = "\n";
+  // The index counter is used to keep aggregated and non-aggregated files in
+  // order by weight.
+  $index = 0;
+  $processed[0] = '';
   $files = array();
   $preprocess_js = (variable_get('preprocess_js', FALSE) && (!defined('MAINTENANCE_MODE') || MAINTENANCE_MODE != 'update'));
   $directory = file_directory_path('public');
@@ -3628,7 +3629,7 @@ function drupal_get_js($scope = 'header', $javascript = NULL) {
   // URL changed. Files that should not be cached (see drupal_add_js())
   // get REQUEST_TIME as query-string instead, to enforce reload on every
   // page request.
-  $query_string = '?' . substr(variable_get('css_js_query_string', '0'), 0, 1);
+  $default_query_string = '?' . substr(variable_get('css_js_query_string', '0'), 0, 2);
 
   // For inline Javascript to validate as XHTML, all Javascript containing
   // XHTML needs to be wrapped in CDATA. To make that backwards compatible
@@ -3648,6 +3649,12 @@ function drupal_get_js($scope = 'header', $javascript = NULL) {
     ),
   );
   foreach ($items as $item) {
+    if (empty($item['version'])) {
+      $query_string = $default_query_string;
+    }
+    else {
+      $query_string = '?v=' . $item['version'];
+    }
     switch ($item['type']) {
       case 'setting':
         $js_element = $element;
@@ -3675,9 +3682,13 @@ function drupal_get_js($scope = 'header', $javascript = NULL) {
             $js_element['#attributes']['defer'] = 'defer';
           }
           $js_element['#attributes']['src'] = file_create_url($item['data']) . ($item['cache'] ? $query_string : '?' . REQUEST_TIME);
-          $no_preprocess .= theme('html_tag', array('element' => $js_element));
+          $processed[$index] .= theme('html_tag', array('element' => $js_element));
         }
         else {
+          // By increasing the index for each aggregated file, we maintain
+          // the relative ordering ofg JS by weight.
+          $index++;
+          $processed[$index] = '';
           $files[$item['data']] = $item;
         }
         break;
@@ -3698,16 +3709,16 @@ function drupal_get_js($scope = 'header', $javascript = NULL) {
   if ($is_writable && $preprocess_js && count($files) > 0) {
     // Prefix filename to prevent blocking by firewalls which reject files
     // starting with "ad*".
-    $filename = 'js_' . md5(serialize($files) . $query_string) . '.js';
-    $preprocess_file = file_create_url(drupal_build_js_cache($files, $filename));
+    $filename = 'js_' . md5(serialize($files)) . '.js';
+    $preprocess_file = file_create_url(drupal_build_js_cache($files, $filename)) . $default_query_string;
     $js_element = $element;
     $js_element['#attributes']['src'] = $preprocess_file;
-    $preprocessed .= theme('html_tag', array('element' => $js_element)) . "\n";
+    $processed[$index] .= theme('html_tag', array('element' => $js_element)) . "\n";
   }
 
   // Keep the order of JS files consistent as some are preprocessed and others are not.
   // Make sure any inline or JS setting variables appear last after libraries have loaded.
-  return $preprocessed . $no_preprocess . $output;
+  return implode('', $processed) . $output;
 }
 
 /**
@@ -3941,14 +3952,20 @@ function drupal_get_library($module, $name) {
     // Allow modules to alter the module's registered libraries.
     if (!empty($module_libraries)) {
       drupal_alter('library', $module_libraries, $module);
+
+      foreach ($module_libraries as $name => $data) {
+        if (is_array($data)) {
+          // Add default elements to allow for easier processing.
+          $module_libraries[$name] += array('dependencies' => array(), 'js' => array(), 'css' => array());
+          foreach ($module_libraries[$name]['js'] as $file => $options) {
+            $module_libraries[$name]['js'][$file]['version'] = $module_libraries[$name]['version'];
+          }
+        }
+      }
     }
     $libraries[$module] = $module_libraries;
   }
-  if (!empty($libraries[$module][$name]) && is_array($libraries[$module][$name])) {
-    // Add default elements to allow for easier processing.
-    $libraries[$module][$name] += array('dependencies' => array(), 'js' => array(), 'css' => array());
-  }
-  else {
+  if (empty($libraries[$module][$name])) {
     $libraries[$module][$name] = FALSE;
   }
 
@@ -6070,8 +6087,8 @@ function drupal_flush_all_caches() {
  *
  * Changes the character added to all css/js files as dummy query-string,
  * so that all browsers are forced to reload fresh files. We keep
- * 20 characters history (FIFO) to avoid repeats, but only the first
- * (newest) character is actually used on urls, to keep them short.
+ * 20 characters history (FIFO) to avoid repeats, but only the first two
+ * (newest) characters are actually used on urls, to keep them short.
  * This is also called from update.php.
  */
 function _drupal_flush_css_js() {
diff --git modules/system/system.module modules/system/system.module
index 3daced7..44ca5f3 100644
--- modules/system/system.module
+++ modules/system/system.module
@@ -1066,7 +1066,7 @@ function system_library() {
     'website' => 'http://jquery.com',
     'version' => '1.3.2',
     'js' => array(
-      'misc/jquery.js' => array('weight' => JS_LIBRARY - 20),
+      'misc/jquery.js' => array('preprocess' => FALSE, 'weight' => JS_LIBRARY - 20),
     ),
   );
 
@@ -1076,7 +1076,7 @@ function system_library() {
     'website' => 'http://plugins.jquery.com/project/once',
     'version' => '1.2',
     'js' => array(
-      'misc/jquery.once.js' => array('weight' => JS_LIBRARY - 19),
+      'misc/jquery.once.js' => array('preprocess' => FALSE, 'weight' => JS_LIBRARY - 19),
     ),
   );
 
@@ -1096,7 +1096,7 @@ function system_library() {
     'website' => 'http://benalman.com/projects/jquery-bbq-plugin/',
     'version' => '1.0.2',
     'js' => array(
-      'misc/jquery.ba-bbq.js',
+      'misc/jquery.ba-bbq.js' => array(),
     ),
   );