The author of the article recognizes there's a problem, but is less clear on how to go about solving it. A clue is in this article by Erik Naggum: http://naggum.no/erik/complexity.html
Dan Ingalls once wrote: "Operating System: An operating system is a collection of things that don't fit into a language. There shouldn't be one." What he meant is we should migrate the functionality of the operating system into the programming language. This is possible if there's a REPL or something similar, so no need for the shell or command line. The language should be image-based, so no need for a file system. So, a bit like Squeak, or a Lisp with a structure editor.
There's still a gap between the processor and the language, which should be eliminated by making the processor run the language directly. This was done in Burroughs mainframes and Lisp machines.
Further up the "stack", software such as word processors and web browsers are at present written entirely separately but have much in common and could share much of their code.