problem with packing files

I have a set of folders, each with their own materials and models folder (similar to an addons folder for GMod). How would I be able to pack materials and models from these folders in to a bsp file? Every program I’ve tried checks for a respective materials and models folder inside the root game folder (e.g. GarrysMod/garrysmod/materials) instead of checking for the materials and models themselves, and thus can not detect my addon-structured materials.

The simplest way would be to tell pakrat, MAN, or VIDE that each of my “addon” folders is a root game directory and to keep packing it. However, this would be inefficient since I have 15+ folders to pack. I could also manually merge all the folders together in to a traditional materials and models folders, but this wouldn’t work with Source Multi-Tool, and it’s more organized in a addon layout. Anybody have a solution?