Load a properties file from current directory.
Properties properties = new Properties();
properties.load(new FileReader(new File(".").getCanonicalPath() + File.separator + "java.properties"));
Write a start script
#! /bin/bash
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cd $scriptdir
java -jar MyExecutable.jar
cd -
Now you can start your configurable java program from any location, e.g. by linking the startscript to /usr/bin/ .