diff --git a/includes/common.inc b/includes/common.inc
index 35a1ccf46c11af27ee151b27b44669c05aafeb9a..5f5f9b66e255cf49c674daca9ef094e97a82a664 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -4555,10 +4555,10 @@ function drupal_flush_all_caches() {
   // If invoked from update.php, we must not update the theme information in the
   // database, or this will result in all themes being disabled.
   if (defined('MAINTENANCE_MODE') && MAINTENANCE_MODE == 'update') {
-    _system_theme_data();
+    _system_get_theme_data();
   }
   else {
-    system_theme_data();
+    system_get_theme_data();
   }
 
   drupal_theme_rebuild();
diff --git a/includes/install.inc b/includes/install.inc
index 5f296477bb90c05e05d35b6c89205f2365dd23ae..03ee3e4bda80acb81bc544299f3fdbdcbb2c708e 100644
--- a/includes/install.inc
+++ b/includes/install.inc
@@ -495,7 +495,7 @@ function drupal_verify_profile($profile, $locale) {
  *   Normally just testing wants to set this to TRUE.
  */
 function drupal_install_modules($module_list = array(), $disable_modules_installed_hook = FALSE) {
-  $files = module_rebuild_cache();
+  $files = system_get_module_data();
   $module_list = array_flip(array_values($module_list));
   do {
     $moved = FALSE;
@@ -592,7 +592,7 @@ function drupal_install_system() {
     ->execute();
   // Now that we've installed things properly, bootstrap the full Drupal environment
   drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
-  module_rebuild_cache();
+  system_get_module_data();
 }
 
 /**
diff --git a/includes/module.inc b/includes/module.inc
index aea3c8f9688d801b5d7eb80eb822d1444211d65f..e0b3ceaad04cea3c773037b92b60b21eaf1403e1 100644
--- a/includes/module.inc
+++ b/includes/module.inc
@@ -75,75 +75,6 @@ function module_list($refresh = FALSE, $sort = FALSE, $fixed_list = NULL) {
   return $list;
 }
 
-/**
- * Rebuild the database cache of module files.
- *
- * @return
- *   The array of filesystem objects used to rebuild the cache.
- */
-function module_rebuild_cache() {
-  // Get current list of modules, including uninstalled modules.
-  $files = drupal_system_listing('/\.module$/', 'modules', 'name', 0);
-
-  // Extract current files from database.
-  system_get_files_database($files, 'module');
-
-  ksort($files);
-
-  // Set defaults for module info
-  $defaults = array(
-    'dependencies' => array(),
-    'dependents' => array(),
-    'description' => '',
-    'package' => 'Other',
-    'version' => NULL,
-    'php' => DRUPAL_MINIMUM_PHP,
-    'files' => array(),
-  );
-
-  foreach ($files as $filepath => $file) {
-    // Look for the info file.
-    $file->info = drupal_parse_info_file(dirname($file->filepath) . '/' . $file->name . '.info');
-
-    // Skip modules that don't provide info.
-    if (empty($file->info)) {
-      unset($files[$filepath]);
-      continue;
-    }
-    // Merge in defaults and save.
-    $files[$filepath]->info = $file->info + $defaults;
-
-    // Invoke hook_system_info_alter() to give installed modules a chance to
-    // modify the data in the .info files if necessary.
-    drupal_alter('system_info', $files[$filepath]->info, $files[$filepath]);
-
-    // Update the contents of the system table:
-    if (isset($file->status) || (isset($file->old_filepath) && $file->old_filepath != $file->filepath)) {
-      db_update('system')
-        ->fields(array(
-            'info' => serialize($files[$filepath]->info),
-            'name' => $file->name,
-            'filename' => $file->filepath))
-        ->condition('filename', $file->old_filepath)
-        ->execute();
-    }
-    else {
-      // This is a new module.
-      $files[$filepath]->status = 0;
-      db_insert('system')
-        ->fields(array(
-            'name' => $file->name,
-            'info' => serialize($files[$filepath]->info),
-            'type' => 'module',
-            'filename' => $file->filepath,
-            'status' => 0))
-        ->execute();
-    }
-  }
-  $files = _module_build_dependencies($files);
-  return $files;
-}
-
 /**
  * Find dependencies any level deep and fill in required by information too.
  *
diff --git a/includes/theme.inc b/includes/theme.inc
index f82e9b00d1d70ea4931033c73acf5e2353c852ec..a723e6fe3de51c732f33c6ffd4ab70922f599432 100644
--- a/includes/theme.inc
+++ b/includes/theme.inc
@@ -528,7 +528,7 @@ function list_themes($refresh = FALSE) {
     }
     else {
       // Scan the installation when the database should not be read.
-      $themes = _system_theme_data();
+      $themes = _system_get_theme_data();
     }
 
     foreach ($themes as $theme) {
diff --git a/includes/theme.maintenance.inc b/includes/theme.maintenance.inc
index 915a5794bed27c6309b298d36df1cbd9b40e5460..3267e1d01b48149d5954c78bc8aea6fd5ee26dac 100644
--- a/includes/theme.maintenance.inc
+++ b/includes/theme.maintenance.inc
@@ -223,7 +223,7 @@ function template_preprocess_maintenance_page(&$variables) {
 
   global $theme;
   // Retrieve the theme data to list all available regions.
-  $theme_data = _system_theme_data();
+  $theme_data = _system_get_theme_data();
   $regions = $theme_data[$theme]->info['regions'];
 
   // Get all region content set with drupal_add_region_content().
diff --git a/install.php b/install.php
index d122cbab8b8de3c6f7fff5bceabe4df4b419dce9..447e38266bd3a03f10ff129692d832c74ab50f02 100644
--- a/install.php
+++ b/install.php
@@ -642,7 +642,7 @@ function install_tasks($profile, $task) {
   // Install profile modules.
   if ($task == 'profile-install') {
     $modules = variable_get('install_profile_modules', array());
-    $files = module_rebuild_cache();
+    $files = system_get_module_data();
     variable_del('install_profile_modules');
     $operations = array();
     foreach ($modules as $module) {
diff --git a/modules/help/help.admin.inc b/modules/help/help.admin.inc
index f3f0041c3ddb3e1d1967baab198d3a44ab07da29..3de153de6356cb6d93281e7bd1d0b6d8d0a7b33e 100644
--- a/modules/help/help.admin.inc
+++ b/modules/help/help.admin.inc
@@ -47,7 +47,7 @@ function help_page($name) {
 
 function help_links_as_list() {
   $empty_arg = drupal_help_arg();
-  $module_info = module_rebuild_cache();
+  $module_info = system_get_module_data();
 
   $modules = array();
   foreach (module_implements('help', TRUE) as $module) {
diff --git a/modules/simpletest/simpletest.module b/modules/simpletest/simpletest.module
index 91d82aa86882d230554980457c5a89c468a2a3a3..1300c24169d60b04f7a5468f4fab18c53a656e45 100644
--- a/modules/simpletest/simpletest.module
+++ b/modules/simpletest/simpletest.module
@@ -211,7 +211,7 @@ function simpletest_get_all_tests() {
   if (!isset($classes)) {
     require_once DRUPAL_ROOT . '/' . drupal_get_path('module', 'simpletest') . '/drupal_web_test_case.php';
     $files = array();
-    foreach (array_keys(module_rebuild_cache()) as $module) {
+    foreach (array_keys(system_get_module_data()) as $module) {
       $module_path = drupal_get_path('module', $module);
       $test = $module_path . "/$module.test";
       if (file_exists($test)) {
diff --git a/modules/system/system.admin.inc b/modules/system/system.admin.inc
index 1ff8bdf9e3624e7f6ee368c589cf593e4f869bbf..5fe1c2424c41de6c6b998df9b4ddffcb7604c5e1 100644
--- a/modules/system/system.admin.inc
+++ b/modules/system/system.admin.inc
@@ -86,7 +86,7 @@ function system_admin_menu_block_page() {
  */
 function system_admin_by_module() {
 
-  $modules = module_rebuild_cache();
+  $modules = system_get_module_data();
   $menu_items = array();
   $help_arg = module_exists('help') ? drupal_help_arg() : FALSE;
 
@@ -141,7 +141,7 @@ function system_settings_overview() {
 function system_themes_form() {
   drupal_clear_css_cache();
 
-  $themes = system_theme_data();
+  $themes = system_get_theme_data();
   uasort($themes, 'system_sort_modules_by_info_name');
 
   $status = array();
@@ -325,7 +325,7 @@ function system_theme_settings(&$form_state, $key = '') {
   if ($key) {
     $settings = theme_get_settings($key);
     $var = str_replace('/', '_', 'theme_' . $key . '_settings');
-    $themes = system_theme_data();
+    $themes = system_get_theme_data();
     $features = $themes[$key]->info['features'];
   }
   else {
@@ -580,7 +580,7 @@ function system_modules($form_state = array()) {
   node_types_rebuild();
   cache_clear_all('schema', 'cache');
   // Get current list of modules.
-  $files = module_rebuild_cache();
+  $files = system_get_module_data();
 
   // Remove hidden modules from display list.
   foreach ($files as $filename => $file) {
@@ -761,7 +761,7 @@ function _system_modules_build_row($info, $extra) {
  * Display confirmation form for required modules.
  *
  * @param $modules
- *   Array of module file objects as returned from module_rebuild_cache().
+ *   Array of module file objects as returned from system_get_module_data().
  * @param $storage
  *   The contents of $form_state['storage']; an array with two
  *   elements: the list of required modules and the list of status
@@ -819,7 +819,7 @@ function system_modules_submit($form, &$form_state) {
 
   // Get a list of all modules, it will be used to find which module requires
   // which.
-  $files = module_rebuild_cache();
+  $files = system_get_module_data();
 
   // The modules to be enabled.
   $modules_to_be_enabled = array();
diff --git a/modules/system/system.api.php b/modules/system/system.api.php
index 0fa5aeea350d13f7b24229aa65dbdecf135db436..0efcedbc3536136a8e8f1da5fd8b8c23f27380da 100644
--- a/modules/system/system.api.php
+++ b/modules/system/system.api.php
@@ -530,7 +530,7 @@ function hook_mail_alter(&$message) {
 /**
  * Alter the information parsed from module and theme .info files
  *
- * This hook is invoked in  module_rebuild_cache() and in system_theme_data().
+ * This hook is invoked in _system_get_module_data() and in _system_get_theme_data().
  * A module may implement this hook in order to add to or alter the data
  * generated by reading the .info file with drupal_parse_info_file().
  *
diff --git a/modules/system/system.install b/modules/system/system.install
index 8f856e1d79bf836d33450cab63d4e05c86059da8..5a68e7007e10783971803fbe6b086b55560d048b 100644
--- a/modules/system/system.install
+++ b/modules/system/system.install
@@ -353,7 +353,7 @@ function system_install() {
   }
 
   // Load system theme data appropriately.
-  system_theme_data();
+  system_get_theme_data();
 
   // Inserting uid 0 here confuses MySQL -- the next user might be created as
   // uid 2 which is not what we want. So we insert the first user here, the
@@ -1542,8 +1542,8 @@ function system_update_6008() {
   db_drop_field($ret, 'system', 'description');
 
   // Rebuild system table contents.
-  module_rebuild_cache();
-  system_theme_data();
+  system_get_module_data();
+  system_get_theme_data();
 
   return $ret;
 }
@@ -1614,8 +1614,8 @@ function system_update_6012() {
  */
 function system_update_6013() {
   // Rebuild system table contents.
-  module_rebuild_cache();
-  system_theme_data();
+  system_get_module_data();
+  system_get_theme_data();
 
   return array(array('success' => TRUE, 'query' => 'Cache rebuilt.'));
 }
diff --git a/modules/system/system.module b/modules/system/system.module
index 767981c82efedd39956b5f42b8cfc955b4ac5f4e..4635a3d3f76d8a831fa9e911914211d7a29cef00 100644
--- a/modules/system/system.module
+++ b/modules/system/system.module
@@ -1159,9 +1159,8 @@ function system_get_files_database(&$files, $type) {
   foreach ($result as $file) {
     if (isset($files[$file->name]) && is_object($files[$file->name])) {
       $file->filepath = $file->filename;
-      $file->old_filepath = $file->filepath;
       foreach ($file as $key => $value) {
-        if (!isset($files[$file->name]) || !isset($files[$file->name]->$key)) {
+        if (!isset($files[$file->name]->key)) {
           $files[$file->name]->$key = $value;
         }
       }
@@ -1170,75 +1169,139 @@ function system_get_files_database(&$files, $type) {
 }
 
 /**
- * Prepare defaults for themes.
- *
- * @return
- *   An array of default themes settings.
+ * Updates the records in the system table based on the files array.
+ * 
+ * @param $files
+ *   An array of files.
+ * @param $type
+ *   The type of the files.
  */
-function system_theme_default() {
-  return array(
-    'regions' => array(
-      'left' => 'Left sidebar',
-      'right' => 'Right sidebar',
-      'content' => 'Content',
-      'header' => 'Header',
-      'footer' => 'Footer',
-      'highlight' => 'Highlighted content',
-      'help' => 'Help',
-    ),
-    'description' => '',
-    'features' => array(
-      'comment_user_picture',
-      'comment_user_verification',
-      'favicon',
-      'logo',
-      'name',
-      'node_user_picture',
-      'search',
-      'slogan',
-      'main_menu',
-      'secondary_menu',
-    ),
-    'screenshot' => 'screenshot.png',
-    'php' => DRUPAL_MINIMUM_PHP,
-  );
+function system_update_files_database(&$files, $type) {
+  $result = db_query("SELECT * FROM {system} WHERE type = :type", array(':type' => $type));
+
+  // Add all files that need to be deleted to a DatabaseCondition.
+  $delete = db_or();
+  foreach ($result as $file) {
+    if (isset($files[$file->name]) && is_object($files[$file->name])) {
+      // Keep the old filename from the database in case the file has moved.
+      $old_filename = $file->filename;
+
+      $updated_fields = array();
+
+      // Handle info specially, compare the serialized value.
+      $serialized_info = serialize($files[$file->name]->info);
+      if ($serialized_info != $file->info) {
+        $updated_fields['info'] = $serialized_info;
+      }
+      unset($file->info);
+
+      // Scan remaining fields to find only the updated values.
+      foreach ($file as $key => $value) {
+        if (isset($files[$file->name]->$key) && $files[$file->name]->$key != $value) {
+          $updated_fields[$key] = $files[$file->name]->$key;
+        }
+      }
+
+      // Update the record.
+      if (count($updated_fields)) {
+        db_update('system')
+          ->fields($updated_fields)
+          ->condition('filename', $old_filename)
+          ->execute();
+      }
+
+      // Indiciate that the file exists already.
+      $files[$file->name]->exists = TRUE;
+    }
+    else {
+      // File is not found in file system, so delete record from the system table.
+      $delete->condition('filename', $file->filename);
+    }
+  }
+
+  if (count($delete) > 0) {
+    // Delete all missing files from the system table
+    db_delete('system')
+      ->condition($delete)
+      ->execute();
+  }
+
+  // All remaining files are not in the system table, so we need to add them.
+  $query = db_insert('system')->fields(array('filename', 'name', 'type', 'owner', 'info'));
+  foreach($files as &$file) {
+    if (isset($file->exists)) {
+      unset($file->exists);
+    }
+    else {
+      $query->values(array(
+        'filename' => $file->filepath,
+        'name' => $file->name,
+        'type' => $type,
+        'owner' => isset($file->owner) ? $file->owner : '',
+        'info' => serialize($file->info),
+      ));
+      $file->type = $type;
+      $file->status = 0;
+      $file->schema_version = -1;
+    }
+  }
+  $query->execute();
 }
 
 /**
- * Collect data about all currently available themes.
+ * Helper function to scan and collect module .info data.
  *
  * @return
- *   Array of all available themes and their data.
+ *   An associative array of module information.
  */
-function system_theme_data() {
-  // Scan the installation theme .info files and their engines.
-  $themes = _system_theme_data();
+function _system_get_module_data() {
+  // Find modules
+  $modules = drupal_system_listing('/\.module$/', 'modules', 'name', 0);
 
-  // Extract current files from database.
-  system_get_files_database($themes, 'theme');
+  // Set defaults for module info.
+  $defaults = array(
+    'dependencies' => array(),
+    'dependents' => array(),
+    'description' => '',
+    'version' => NULL,
+    'php' => DRUPAL_MINIMUM_PHP,
+  );
 
-  db_delete('system')
-    ->condition('type', 'theme')
-    ->execute();
+  // Read info files for each module.
+  foreach ($modules as $key => $module) {
+    // Look for the info file.
+    $module->info = drupal_parse_info_file(dirname($module->filepath) . '/' . $module->name . '.info');
 
-  $query = db_insert('system')->fields(array('name', 'owner', 'info', 'type', 'filename', 'status'));
-  foreach ($themes as $theme) {
-    if (!isset($theme->owner)) {
-      $theme->owner = '';
+    // Skip modules that don't provide info.
+    if (empty($module->info)) {
+      unset($modules[$key]);
+      continue;
     }
 
-    $query->values(array(
-      'name' => $theme->name,
-      'owner' => $theme->owner,
-      'info' => serialize($theme->info),
-      'type' => 'theme',
-      'filename' => $theme->filename,
-      'status' => isset($theme->status) ? $theme->status : 0,
-    ));
+    // Merge in defaults and save.
+    $modules[$key]->info = $module->info + $defaults;
+
+    // Invoke hook_system_info_alter() to give installed modules a chance to
+    // modify the data in the .info files if necessary.
+    drupal_alter('system_info', $modules[$key]->info, $modules[$key]);
   }
-  $query->execute();
 
-  return $themes;
+  return $modules;
+}
+
+/**
+ * Collect data about all currently available modules.
+ *
+ * @return
+ *   Array of all available modules and their data.
+ */
+function system_get_module_data() {
+  $modules = _system_get_module_data();
+  ksort($modules);
+  system_get_files_database($modules, 'module');
+  system_update_files_database($modules, 'module');
+  $modules = _module_build_dependencies($modules);
+  return $modules;
 }
 
 /**
@@ -1247,7 +1310,7 @@ function system_theme_data() {
  * @return
  *   An associative array of themes information.
  */
-function _system_theme_data() {
+function _system_get_theme_data() {
   static $themes_info = array();
 
   if (empty($themes_info)) {
@@ -1256,7 +1319,37 @@ function _system_theme_data() {
     // Find theme engines
     $engines = drupal_system_listing('/\.engine$/', 'themes/engines');
 
-    $defaults = system_theme_default();
+    // Set defaults for theme info.
+    $defaults = array(
+      'regions' => array(
+        'left' => 'Left sidebar',
+        'right' => 'Right sidebar',
+        'content' => 'Content',
+        'header' => 'Header',
+        'footer' => 'Footer',
+        'highlight' => 'Highlighted content',
+        'help' => 'Help',
+      ),
+      'description' => '',
+      'features' => array(
+        'comment_user_picture',
+        'favicon',
+        'mission',
+        'logo',
+        'name',
+        'node_user_picture',
+        'search',
+        'slogan',
+        'main_menu',
+        'secondary_menu',
+      ),
+      'stylesheets' => array(
+        'all' => array('style.css')
+      ),
+      'scripts' => array('script.js'),
+      'screenshot' => 'screenshot.png',
+      'php' => DRUPAL_MINIMUM_PHP,
+    );
 
     $sub_themes = array();
     // Read info files for each theme
@@ -1339,6 +1432,20 @@ function _system_theme_data() {
   return $themes_info;
 }
 
+/**
+ * Collect data about all currently available themes.
+ *
+ * @return
+ *   Array of all available themes and their data.
+ */
+function system_get_theme_data() {
+  $themes = _system_get_theme_data();
+  ksort($themes);
+  system_get_files_database($themes, 'theme');
+  system_update_files_database($themes, 'theme');
+  return $themes;
+}
+
 /**
  * Recursive function to find the top level base theme. Themes can inherit
  * templates and function implementations from earlier themes.
diff --git a/modules/update/update.compare.inc b/modules/update/update.compare.inc
index e2186e7f296260692ea3025a46d9832277b70910..c198c7d49f2546c9c9b91100ae7431ed2e40ba1e 100644
--- a/modules/update/update.compare.inc
+++ b/modules/update/update.compare.inc
@@ -36,8 +36,8 @@ function update_get_projects() {
     $projects = update_project_cache('update_project_projects');
     if (empty($projects)) {
       // Still empty, so we have to rebuild the cache.
-      _update_process_info_list($projects, module_rebuild_cache(), 'module');
-      _update_process_info_list($projects, system_theme_data(), 'theme');
+      _update_process_info_list($projects, system_get_module_data(), 'module');
+      _update_process_info_list($projects, system_get_theme_data(), 'theme');
       // Allow other modules to alter projects before fetching and comparing.
       drupal_alter('update_projects', $projects);
       // Cache the site's project data for at most 1 hour.
diff --git a/update.php b/update.php
index a0fb6d9248c259227fa04c6de33ee9b3346fd34b..95ff18d5157d4cb77f76213addaa360d70c2b17d 100644
--- a/update.php
+++ b/update.php
@@ -499,8 +499,8 @@ function update_check_incompatibility($name, $type = 'module') {
 
   // Store values of expensive functions for future use.
   if (empty($themes) || empty($modules)) {
-    $themes = _system_theme_data();
-    $modules = module_rebuild_cache();
+    $themes = _system_get_theme_data();
+    $modules = system_get_module_data();
   }
 
   if ($type == 'module' && isset($modules[$name])) {