I've been considering writing a "programming system of the future, backwards-compatible with the cranky programmers of today" by having just such a relational (or key-value) underlying representation... and then a FUSE server that presents an editable filesystem+text view of it.

Among a thousand other benefits, the "cutest" one is that all code gets canonicalized on save. The filesystem will literally reject a write(3) that can't be translated into a valid AST to be stored into the underlying DB. It's like a super-powered version of running "go fmt" as a git pre-commit hook.