If you want to save a file and modify it programmatically I would suggest you to store it in this path:
/data/data/com.yourpackage.app/punt.xml
I have never worked with Jdom2, but you can have access to it by adding these lines of code:
File puntFile= new File("data/data/com.yourpackage.app/punt.xml");
FileOutputStream fos = new FileOutputStream(puntFile);
xmlOutput.output(puntu, fos);
You can also see the file in DDMS in file explorer. Just follow that path.
I can't understand if you want to save and edit the file during the process of your application or just save it somewhere before the app starts and edit it afterwords. If so, please give more details about that.
Hope I helped...