Folders and registry keys have special configuration dialog which allows users to configure 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 will try to use reasonable defaults based on type and location of a resource, to provide the best possible results that should work for most of the packages.