Revert "Join the emu thread in Core::Stop. Get rid of Core::Shutdown which did that before."

This reverts commit ba664b3293.

Added documentation to Core::Shutdown() to prevent breaking changes.

Source/Core/DolphinWX/MainAndroid.cpp

@@ -622,6 +622,7 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_Run(JNIEnv *
 			updateMainFrameEvent.Wait();
 	}
 
+	Core::Shutdown();
 	UICommon::Shutdown();
 	ANativeWindow_release(surf);
 }