You don't have to use the braindead IDE-style projects wrapper. Just put your design in a directory and add schematics, pcb layouts, documentation, and netlists as needed; put common components, footprints, and firmware in subdirectories. Or structure it however it makes most sense. The project stuff adds absolutely nothing and just gets in the way, making it difficult for instance to edit two layouts side by side to make sure their mounting holes and a mezzanine connector lines up, or any number of other common uses.