Add additional methods for to the CommandBuilder for passing YAML files

The StandaloneCommandBuilder has a setYamlFiles(Path[]), but this should likely be varargs for better usability. There should also be one to set the values based on a collection. There is also missing JavaDoc and this could add the --yaml argument more than once which is not supported. This is a public facing API that should be documented and easy to use. We should add some additional methods as well as update the JavaDoc.