I would personally prefer if the command-line options had priority over anything else.  You could do that by making the loop create new conf's and using `conf.setIfUnset(fileConf.get(...))` instead of `addResource(file)`.  It's more code but I think the behavior would be better.

And actually, I think most people would expect the first file they specified to take the next priority.  That's the opposite behavior to what you have but all you've need to do is iterate over those `,`-separated lists in reverse order to achieve the right effect.