diff -u b/core/includes/common.inc b/core/includes/common.inc
--- b/core/includes/common.inc
+++ b/core/includes/common.inc
@@ -7289,17 +7289,31 @@
 }
 
 /**
- * Flushes and resets all caches, and rebuilds data structures.
+ * Flushes all persistent caches, resets all variables, and rebuilds all data structures.
  *
- * At times, it is necessary to "re-initialize" the entire system to account for
+ * At times, it is necessary to re-initialize the entire system to account for
  * changed or new code. This function:
- * - Clears all persistent caches (invoking hook_cache_flush()).
- * - Clears all static caches.
- * - Clears asset file caches.
- * - Updates the system with latest extension information.
- * - Rebuilds and synchronizes data structures (invoking hook_rebuild()).
+ * - Clears all persistent caches (invoking hook_cache_flush()), which always
+ *   includes:
+ *   - The bootstrap cache bin containing base system, module system, and theme
+ *     system information.
+ *   - The common 'cache' cache bin containing arbitrary caches.
+ *   - The page cache.
+ *   - The URL alias path cache.
+ * - Resets all static variables that have been defined via drupal_static().
+ * - Clears asset (JS/CSS) file caches.
+ * - Updates the system with latest information about extensions (modules and
+ *   themes).
+ * - Updates the bootstrap flag for modules implementing bootstrap_hooks().
+ * - Rebuilds the full database schema information (invoking hook_schema()).
+ * - Rebuilds data structures of all modules (invoking hook_rebuild()).
  * - Rebuilds the menu router.
  *
+ * This means the entire system is reset to be effectively empty. After that is
+ * guaranteed, information about the currently active code is updated, and
+ * rebuild operations are successively called in order to synchronize the active
+ * system according to the current information defined in code.
+ *
  * All modules need to ensure that all of their caches are flushed when
  * hook_cache_flush() is invoked; any previously known information must no
  * longer exist. All following hook_rebuild() operations must be based on fresh
@@ -7322,7 +7336,7 @@
  */
 function drupal_flush_all_caches() {
   // Flush all persistent caches.
-  // This is executed based on "previously" known information, which is
+  // This is executed based on old/previously known information, which is
   // sufficient, since new extensions cannot have any primed caches yet.
   foreach (module_invoke_all('cache_flush') as $bin) {
     cache($bin)->flush();
@@ -7361,9 +7375,6 @@
   // Rebuild all information based on new module data.
   module_invoke_all('rebuild');
 
-  // Synchronize to catch any actions that were added or removed.
-  actions_synchronize();
-
   // Rebuild the menu router based on all rebuilt data.
   // Important: This rebuild must happen last, so the menu router is guaranteed
   // to be based on up to date information.
diff -u b/core/modules/system/system.api.php b/core/modules/system/system.api.php
--- b/core/modules/system/system.api.php
+++ b/core/modules/system/system.api.php
@@ -2125,6 +2125,11 @@
  * system is known to return current information, so your module can safely rely
  * on all available data to rebuild its own.
  *
+ * The menu router is the only exception regarding rebuilt data; it is only
+ * rebuilt after all hook_rebuild() implementations have been invoked. That
+ * ensures that hook_menu() implementations and the final router rebuild can
+ * rely on all data being returned by all modules.
+ *
  * @see hook_cache_flush()
  * @see drupal_flush_all_caches()
  */
diff -u b/core/modules/system/system.module b/core/modules/system/system.module
--- b/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -3101,6 +3101,8 @@
 function system_rebuild() {
   // Rebuild list of date formats.
   system_date_formats_rebuild();
+  // Synchronize any actions that were added or removed.
+  actions_synchronize();
 }
 
 /**