My own biggest beef with the article is it entirely misses the deep point of Marie Kondo's work, which is about efficiency and joy. If the article is not actually a response to her philosophy and definition of tidiness, and just needed a cute title, well, that's confusing at the very least. The commenters who point out that codebases, for example, need to be reasonable for humans to work in, or that it sure is easier to change source code than a compiled binary, are on the right track.
Kondo's method is all about identifying the clutter _that is actually clutter_, and deleting it. Would you rather maintain a program that's 1000 lines, or 100? If the 1000-line program was written by you, for you, over the course of your life, and by your own admission is extremely messy and moderately unpleasant to deal with, containing lots of unused stuff, yet you run it, and modify it, every day, no one is going to force you to clean it up, but you can find joy in doing so.