Thanks, I understood the problem better.
So, I have an idea that could merge layers to tags: Evernote.
I love this app and it is essential in my work.
Evernote uses tags as if they were nested folders.
What’s the benefit? You can have a classic tree system where the tags are the folder names.
But you can also assign multiple tags to an item, so it’s easy to find an item.
Example: in the search engine I write three tags
(Sprites, Level 1, Enemies) and find everything immediately!
So… no folders, just tags! 