Config: Don't clear callbacks on shutdown

This fixes a problem that started happening in CoreTimingTest after the
previous commit. CPUThreadConfigCallback registers a Config callback
only once per run of the process, but CoreTimingTest calls
Config::Shutdown after each test, and Config::Shutdown was clearing all
callbacks, preventing the callback from running after that.

Source/Core/Common/Config/Config.cpp

@@ -138,7 +138,6 @@ void Shutdown()
   WriteLock lock(s_layers_rw_lock);
 
   s_layers.clear();
-  s_callbacks.clear();
 }
 
 void ClearCurrentRunLayer()