Comment by Twey

From two directions:

There are programming languages that store code in some kind of non-hierarchical format. For example, Unison (https://www.unison-lang.org/) stores code in a database just as you suggest, and projects it down to text for editing. A more established example is probably Smalltalk, which stores the code as part of an image that is edited live in the Smalltalk environment.

On the other side, you can have filesystems that are not hierarchical, for example semantic filesystems like Tagsistant for Linux — these can be used for more flexible relationships between any kind of file, not just code.