Native Oberon.

No, I'm kidding, but Native Oberon is pretty much this as a (research) operating system; the interface is a bunch of text editor panes, you type out commands and run them by middle-clicking on them, commands tend to produce output in the form of further commands you can run, and you can save these panes as files at any time.

It's almost like a generalised version of the core operating system shown in The Mother Of All Demos.

I believe this is it isn't it? https://github.com/trogdoro/xiki

Acme,or Plan9 terminal, EMACS Org Mode

From the brief time I spent with Emacs, I think its shell integration can work like that, but you'll need to write some elisp code to get all the features he shows for xiki.