If the jar doesn't represent your main executable, then I would just pass the relevant methods a Properties object directly. Make the main executable responsible for loading the file.
getResourceAsStream() requires the resource to be on the class path. You can make a separate source folder for your config files, and put it on the class path. If you don't want to do that, you should use a FileInputStream instead.
Personally I think the best way to do this is to use the class path correctly. Add the config directory to your project, have maven copy it to the output directory, and add the config directory to the class path in your jar's manifest.
You can now use the getResourceAsStream method to load the properties file, which I think is more robust than using files.
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