elder config settings not registering properly

[AO33]

When trying to run the algorithm using the following command (passing in my own config file) a few of the options are ignored.

• elder -c my_elder_config.yaml bestmach

• The program will output the results to the current working directory instead of to the specified output_dir

• The program also ignores the multiprocess arguments and seems to always use multiprocess even if set to false