For this method on line 25(github doesn't let me comment on things that I noticed)
  private String askUserForPort(int port, String portDescription) throws IOException {              
    System.out.println("Please enter a port for " + portDescription);                               
    System.out.println("or press enter to use suggestion: " + port);                                
    return mReader.readLine();                                                                      
  }       

This should really just put the suggestion in [].  It's pretty standard for linux tools to use square brackets to imply defaults.