citra-qt: Move system shutdown to run inside EmuThread

This stops (for some reason sporadic) crashes and OpenGL errors during
shutdown, when the OpenGL renderer tries to clean up objects from the
UI thread, which has no OpenGL context active.

src/citra_qt/bootmanager.cpp

@@ -72,6 +72,9 @@ void EmuThread::run() {
         }
     }
 
+    // Shutdown the core emulation
+    System::Shutdown();
+
     MicroProfileOnThreadExit();
 
     render_window->moveContext();