When running an app created by jpackage, the current working directory is set to the "app" directory.

confirmed building simple app-image from app with the following source:
import java.io.*;


public class pwd {
    public static void main (String[] args) {
        try {
            String current = new java.io.File( "." ).getCanonicalPath();
            System.out.println("Current dir:"+current);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}

It would be expected that an app run from a command line should have the current working directory of the shell that invoked it.