[WFCORE-220] Set system properties in the CLI entry point

The original two PR's, #249 and #260, did this from the scripts. It's difficult to ensure that scripts parse the parameters correctly. This PR reverts the original two and sets the system properties in the CLI entry point. @aloubyansky needs to approve this.
One thing that probably should be considered is whether these should override what's in the `--properties` file. A collection of keys should probably be kept and one should not be allowed to override the other.