My bundling looks like this and I call the resources like this. All works well when run from Eclipse, though when exported as a runnable Jar. The program appears to not be able to reference the resources
Question
Why are my assets not accessible when packaged?
File doesn't work well with jars, because the file system isn't set up to see into jars. If you use URL's to address your resources you should be fine.
EDIT: adding example.
Assuming your linked address phrase is correct (since the code works in Eclipse, that seems likely), the following should get you a working URL.
URL url = MapLoader.class.getResource("assets/xml/maps.xml");
What you do next depends on the class and method where you use this as an argument. If you check the API for the class & method where you are using the File as an argument, chances are, there will be a similar method that uses a URL.