I have honestly never seen a single person have any issues with directories, nested or no, and as old as the concept might be, the people I interact with seem to be able to handle it just fine. Contrary to the broad strokes made in the article, nested folders really aren't all that complicated conceptually, especially not when compared to, say, the mouse (indirect manipulation), the concept of applications (totally arbitrary), and dozens of other accepted computing concepts.
In fact, a complete absence of a regular accessible directory structure seems to create more problems than it supposedly solves. Applications on the poster child for this concept, iOS, are islands, and the files within them are not easily shared, which leads to all sorts of different problems. Then there's the issue of not knowing where a certain file is; instead of having your own structure, tailor-made for you because you created it in the first place, you now have to remember which application created what file. And what happens when it's in an application you deleted? It's all needlessly complicated.
It seems to me that directory structures are something that some people desperately want to be difficult, but in reality, really aren't. It's a conceptual problem that, in reality, doesn't exist. I've never heard anyone say "Instead of tucked away in folders I can remember, I want all my files to be in one big mess of a pile that only a searching tool can make sense out of, so that I, consequently, have to remember each and every file name or parts of its content". I also have never heard people say "I wish all my files were strictly tied to individual applications, making it very hard to move them around or take them with me."
All this talk about directory structures as if they were the seed of the devil annoys me, because it seems like the success of iOS makes it a legitimate position, as if iOS' success is 100% - or even 10% - based on how it
doesn't handles files. The fact that virtually everyone I know with an iPhone or iPad emails files to themselves to get them on those devices illustrates just how far we've regressed.
Emailing files to get them on devices? Seriously?
Directory structures are not evil, and they're not hard to understand just because some people believe they should be. Like cupboards, Tupperware, boxes, closets, pockets, wallets, and about a gazillion other products, directories allow us to organise our stuff, and that's a concept as old as time itself. Throwing them away just because Steve Jobs hated them is not only short-sighted, it's destructive, and makes computing more complicated, not less.
Right, so this paragraph wasn't supposed to be here, but this just hit me the moment I wanted to press publish: making files harder to move around? Making it harder to find them? Making it harder to take them with you? It's been staring me in the face this whole time.