Make CLI "--env" args take precedence over file

Make `helios create` CLI "--env" args take precedence over
env args with redundant keys specified in helios job config file.
Minor nitpick, but I think it would be a little more efficient to add all the variables from the file first, and then just overwrite them with values from the CLI. It would be a few less lookups in the hashmap. Not a big deal, so I'll still +1 if you don't feel like changing.