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Hi Brett, have a look at this page that goes into great detail about the different ways to classify nodes and the pros/cons of each: https://docs.puppetlabs.com/pe/latest/puppet_assign_configurations.html.

To answer your questions about version control and site.pp/PE console sync - the actions performed in the PE console are not version controlled anywhere in the file system. Also, there is no sync between classes assigned to nodes in site.pp and what appears in PE console and vice-versa. In fact, the classes from each data source are merged together to classify the node. See this page for more info: https://docs.puppetlabs.com/guides/external_nodes.html#what-is-an-enc

Hope that helps, Greg