The way I have structured my folders is from large vague concepts to more precise ones. For example, I have Assets > Prefabs. In the prefabs folder, there are folders for enemies, player characters, environments (which will then be sorted into specific scenes once I have more scenes) and Camera and UI. For now, since the project is small, the enemies folder is just the one older with my enemies and projectiles. My Player Character folder, however, is separated into my knight and healing companion folders. In each of those folders, there is the character prefab, and that character’s projectile prefab. My art folder is separated into materials, textures and fbx files.
Everything else follows a similar pattern. My scripts folder is separated into player, enemies, camera and UI, etc. For me, this works because everything is separated out by “department”. If there’s a scripting issue I know exactly where to look. Art issue? same thing. and since I’m having to switch hats so often, knowing precisely where to look seems to help.
Having said that, I really like Ben’s concept of being able to export a particular part of the game out really easily. If anyone has any suggestions, I’m always open to new ways of doing things if a better idea is presented.