I am talking about “mindmap-like” visual organization, which doesn’t have to be strictly hierarchical. It might not be for everyone, but for me a visual representation of my current knowledge about a certain bucket of literature goes far beyond what a folder/group structure can achieve. It is probably a combination of the bird-eyes view and the ability to use spacial distance to create implicit connections additionaly to the hierarchical structure.
This is not the prettiest example, but it worked for me when writing my last paper:
