I wonder if this might be a situation where the spatial navigation concepts found in the original macOS would be beneficial. It leveraged the user’s spatial and muscle memory to enable quick navigation of the filesystem by giving each directory its own dedicated window with a user-defined size and screen location. The effect is very much like navigating a physical space, with each file and folder having a spatial “path” that’s effortlessly encoded in memory.

While this may not scale well to the complexity of modern filesystems, it might work well for a stylus-based digital notetaking device.