use App.instance() in Application.initialize_subapp

This way later calls to App.instance() will return the running
application, whereas calling App() would create an isolated
Application object.

IPython/config/application.py

@@ -274,8 +274,10 b' class Application(SingletonConfigurable):'
         if isinstance(subapp, basestring):
             subapp = import_item(subapp)
         
+        # clear existing instances
+        self.__class__.clear_instance()
         # instantiate
-        self.subapp = subapp()
+        self.subapp = subapp.instance()
         # and initialize subapp
         self.subapp.initialize(argv)