The best example I'm aware of is probably Smalltalk coupled with monticello version control and a solid object database like gemstone/s (I'm not aware of a real open/free workalike for the last part).

That's not not say relational or logic databases aren't useful - but it's more difficult to manage the data, query code and program code in one integrated system if the database takes the form of an external server. That said, Ms visual studio and the SQL db gui does a pretty good job of presenting a somewhat coherent environment.

I used to be strongly in the Linux/Unix camp - thinking that the datastore we call the filsystem is a good abstraction. But I've come to believe that even the strong legacy of user familiarity isn't a good enough reason to stick with it. Even if we were a little bit more serious and at least went all plan9 - rather than the half-hearted state of Linux/Unix (everything is a file, or a database file, or a binary file or an archive of a filsystem or...).

That said a "filsystem" might very well still be a decent building block for a higher level system (with decent search, for example).

But yeah, I don't think jupyter is the be all, end all of development. But it is an interesting way to move legacy programming environments forward in a low friction manner.