Organize files attached to a node into folders
Just make a taxonomy vocabulary to simulate the folder structure. Install File Entity module. It makes fieldable files, so you can attach taxonomy for the file own - with the module Media you can do that during editing the node.

To display files grouped by folders, you can make a view to do that, and use EVA to embed it into the node. In the view you have to make a 'File' based view, just add a relationship to the node, and add a Content Id contextual filter, which use that relationship.