Folders and registry keys have a special configuration dialog which allows users to configure the desired level of merging when building App-V 4.6/5.x/Thin-App projects. To trigger the settings, right-click a registry key or a folder and go to the ISOLATION tab:
When no custom isolation is used, RayPack tries to use reasonable defaults based on type and location of a resource to provide the best possible results that should work for most of packages.