All of this is possible without throwing out any existing technology (at least for Linux and Windows; if Apple doesn't envision a use case for something it's very likely never going to exist on their platform). Linux compositors have the ability to manipulate the window however the hell they want, and while it's not as popular as it used to be, you can change the default shell on Windows and use any window manager you can program. A database filesystem is two parts: a database and a filesystem. Instead of throwing out the filesystem which works just fine, add a database which offers views into the filesystem. The author is really woe-is-me about how an audio player doesn't have a database of mp3s, but that's something that is done all the time. Why do we have to throw out the filesystem just to have database queries? And if it's because every app has to have their own database- no they don't. If you're going to rewrite all the apps anyways, then rewrite them to use the same database. Problem solved. The hardest concept to implement in this article would be the author's idea of modern GUIs, but it can certainly be done.

On top of this, the trade-off of creating an entirely new OS is enormous. Sure, you can make an OS with no apps because it's not compatible with anything that's been created before, and then you can add your own editor and your own web browser and whatever. And people who only need those things will love it. But if you need something that the OS developer didn't implement, you're screwed. You want to play a game? Sorry. You want to run the software that your school or business requires? Sorry. Seriously, don't throw out every damn thing ever made just to make a better suite of default apps.