Application: extract the auto exit behavior into a separate method from __removeWindow()

This will allow OpenFL to override the behavior based on the NativeApplication class.

src/lime/app/Application.hx

@@ -549,6 +549,12 @@ class Application extends Module
 			__windowByID.remove(window.id);
 			window.close();
 
+			__checkForAllWindowsClosed();
+		}
+	}
+
+	@:noCompletion private function __checkForAllWindowsClosed():Void
+	{
 		if (__windows.length == 0)
 		{
 			#if !lime_doc_gen
@@ -556,7 +562,6 @@ class Application extends Module
 			#end
 		}
 	}
-	}
 
 	@:noCompletion private function __onGamepadConnect(gamepad:Gamepad):Void
 	{