MDL-41437 fix plugin install issues

This patch prevents inclusion of settings from plugin that or not yet installed or upgraded,
this matches the original logic where we were using the modules table.

lib/adminlib.php

@@ -6419,8 +6419,10 @@ function admin_get_root($reload=false, $requirefulltree=true) {
  */
 function admin_apply_default_settings($node=NULL, $unconditional=true) {
     global $CFG;
+    require_once($CFG->libdir.'/pluginlib.php');
 
     if (is_null($node)) {
+        plugin_manager::reset_caches();
         $node = admin_get_root(true, true);
     }
 
@@ -6445,6 +6447,8 @@ function admin_apply_default_settings($node=NULL, $unconditional=true) {
                 $setting->write_setting_flags(null);
             }
         }
+    // Just in case somebody modifies the list of active plugins directly.
+    plugin_manager::reset_caches();
 }
 
 /**