Fixed so options from config files and command lines actually work:

Fixed so options from config files and command lines actually work:
  * 'get_command_obj()' now sets command attributes based on
    the 'command_options' dictionary
  * some typos fixed
  * kludged 'parse_config_files()' to re-initialize the ConfigParser
    instance after each file, so we know for sure which config
    file each option comes form
  * added lots of handy debugging output