One thing I experimented with was writing a tag-based filesystem for that sort of thing. Imagine, e.g., using an entity component system and being able to choose a view that does a refactor across all entities or one that hones in on some cohesive slice of functionality.

In practice, it wound up not quite being worth it (the concept requires the same file to "exist" in multiple locations for that idea to work with all your other tools in a way that actually exploits tags, but then when you reference a given file (e.g., to import it) that needs to be some sort of canonical name in the TFS so that on `cd`-esque operations you can reference the "right" one -- doable, but not agnostic of the file format, which is the point where I saw this causing more problems than it was solving).

I still think there's something there though, especially if the editing environment, programming language, and/or representation of the programming language could be brought on board (e.g., for any concrete language with a good LSP, you can re-write important statements dynamically).