[xorcist]

> we still use the metaphor of files and folders for organizing our source code

We don't use the metaphor for storing things. What we use is an hierarchical naming scheme. This makes sense for a number of use cases, and has been independently discovered multiple times through the short history of computing.

You may call the nodes files and folders. It is however just a word, a parable for the underlying data structure, which is the physical reality. You could just as easily call it something else. And many people, whose first language is different from yours, probably does.