CDK-668: Update maven plugin to setup DefaultConfiguration.

Previously, properties set in the plugin's configuration were local and
the getDatasetRepository method had to use repository builders to use
the correct file system. This updates the method to create repository
URIs instead and changes the getConf method to update the default
Configuration.
Based on my work trying generate legacy repository URIs, things are very much not consistent. I'll start the mailing list thread.