I might be misunderstanding, but this might be close to onenote if onenote could also contain / represent your file system. I did some serious digging. I found that one can disable auto-arrange in Windows 10, so a folder could hold and arrange files like your desktop can.
I decided that a "desktop" within a window would be a cool solution, maybe someone could leverage Windows 10's virtual desktops for that. MS (and Stardock) has been working on "Sets" where you combine applications together into a tabbed window, but I don't think that is helpful for multitasking as you only see one program at a time.
Two top contender alternatives that I found would be: Nimi Places and Sideslide. Sideslide provides virtual workspaces where you can store related things in a variety of manners, but I have found the learning curve steep and the graphics are a bit off putting to me.