Should DDP obey or modify the config file?

[bethac07]

Since both the config file and the job file have some specified options (ie should preprocessing happen) in common, you could end up in a situation where there is a mismatch. Which of the 3 should be true in this case-

1. Throws an error, user has to fix the mismatch - current behavior
2. Config file overrides job file settings
3. Job file overrides config file settings

cc @jccaicedo