Allow an explicitly provided command-line argument to override the same parameter from the configuration file

[levyj]

Currently, it appears that the value in the configuration file controls if both are provided. It might be useful to allow people to set usual values in the configuration file but override them for a particular job. Actually, the priority (highest to lowest) probably should be:

1. Command-line argument
2. Configuration file
3. Internally stored values (Windows registry or other OS equivalent) entered through the GUI (or possibly another means in the future)