I agree on part of that -- VSCode has a pretty good Node debugger, and you can run it with a listen hook (and therefore set it to run via a npm/yarn package.json script). Similarly, I feel like it's OK for an editor to run a script from the app in an integrated terminal, as long as that script is still accessible from a standard CLI.

Git is complex enough that I don't trust more complex operations (basically anything beyond push, pull, add, and checkout) to be handled by a GUI, but a GUI can make for a great code review tool.