Cannot combine command-line options with config file options

[SolomonShorser-OICR]

Maybe I did something wrong, but the application simply wouldn't run when there was a mix of command-line options and config file options.

Specifically, I used an auth.properties file for databases connection info and then specified a single QA Check to run. It only works when I put the db connection options on the command line, and then it seems to run ALL of the checks, not just the one I specified.

I think there might be some bugs in how command line options and config file values are handled.

[SolomonShorser-OICR]

It's possible that this wasn't a bug but an error in the way it was run...