Note: a brand new version of the ReadCube Papers desktop app for OS X and Windows will be available soon!
Many of our users already have their .PDF files organized into specific folders before they import them into ReadCube Desktop (legacy). If you want your lists to reflect the folder structure on your computer, there is a simple step you need to take before you begin to import your library. In your preferences menu under the "general" tab, all you have to do is select the option to "Create lists during import based on article folders" and your ReadCube will create lists and organize your articles in them appropriately.
If you've already imported your library and want to start from scratch, we suggest selecting the top article, holding shift, then selecting your last article in your library and pressing the delete key. At this point, click and drag all of the folders directly into your ReadCube client and they will this time be organized into lists.