I'm not sure I understand what changes the author is proposing, but it just seems the same as a standard IDE with a slightly more annoying UI.

Code is stored in files. Each file has its own URI (the path). You can access those however you like, a file explorer, terminal, etc.

If you want to interact with a file you (and the AI) can use any of the Linux binaries to interact with it.

Git are also files, you have a convenient binary (git) to decide how and what information to show.

AI should interact with the OS the same as you do but we shouldn't be reinventing the wheel just to make it "AI friendly" the same as we are training autonomous cars in our current roads instead of adapting them for AI cars