The config options that relate to directories should be prefixed dir_ Presently not all of them even include a "dir" as part of the name, and (remarkably search_path_file specifies a directory containing the file search.pro) This means that an admin can sort on config options that affect the system architecture. The paths are independent of the function of their contents and should be easily segregated
2.) Have a config hierarchy
There are dozens of nc directory related config options, even though they could all have the same value. There should be a higher level option that supply the default for all the subordinate options. If one of those options needs its own path, then that config can be set; if the high level option is set in the config.sup, then no subordinate options that are set after that can be used. This way a few configs control the approximately 100 configs that alter where files are located.
3.) Prefix config options with the type of object that is affected by the config when it's possible to do so. lay_ for layer items, fam_t_ for family table items.