The simplest solution is to pass the path as an argument when running the jar.
You can automate this with a shell script (.bat in Windows, .sh anywhere else):
java -jar my-jar.jar .
I used .
to pass the current working directory.
UPDATE
You may want to stick the jar file in a sub-directory so users don't accidentally click it. Your code should also check to make sure that the command line arguments have been supplied, and provide a good error message if the arguments are missing.