For more involved answers, how would you score code length for something like a binary calculator?
Unless there is another mechanism that can be used to reliably and consistently import a "program", the save file is the obvious choice. Yes, that means your score will probably be much higher than other languages. No, there's nothing wrong with that - competition within languages, remember? As commented, you can golf and/or generate the save files manually, which can save some bytes.
Plus, Java won't be the most verbose language anymore.
If you copy something from Algodoo and paste it in notepad, you can see the Thyme code that generates such thing. Also, pasting it back work fine even if it's not standard copy-out text