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The Set System Image VI (and by extension, the Replication and Deployment Tool) have a deployment blacklist. Currently, files on that list are never deployed. It would be helpful if instead, those files, if they exist in the image, were deployed only if they do not already exist on the target. That would make it easier to create a single image that could be used for both an upgrade, where you do not want to overwrite existing configuration files, and for initial setup, where you want to install a default configuration file.
Did I misunderstand something about the way the deployment blacklist works? The documentation says "Files on the blacklist will not be copied from the image to the target" which makes me wonder why you would ever want to include those files in the image at all.