code: public static String[] initialize(String programName, String[] args, String... otherPackages) {
        return initialize(programName, args, new CommandLineParser(), otherPackages);
     }
docs: <p> Initializes the configuration. </p> <p> Looks for a properties (programName.conf) in the classpath, the user
  home directory, and in the run directory to load </p> <p> The command line arguments are parsed and added to the
  configuration. </p>
  
  @param programName   the program name
  @param args          the command line arguments
  @param otherPackages Other packages whose configs we should load
  @return Non config/option parameters from command line