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Systems people tend to do the simplest, reasonable thing that works, then forget about it until it doesn't work anymore. This means that sometimes you'll make design choices that look ugly, but really, they don't matter.

See this talk by Jonathan Blow, the designer and programmer behind Braid: http://news.ycombinator.com/item?id=2689999

The author points out it was a bug that caused this, not a valid state. I think they should probably be using sqlite anyways though.

Indeed,

Sure, you can find out a lot by doing things you really shouldn't do, like using the directory system as k/v store.

But in the end, you should still learn the lesson that it is really a bad idea.