> I have had wanted to access the filesystem via JavaScript, just as I do via ruby or python

There are some (limited) ways to do so now: https://developer.mozilla.org/en-US/docs/Web/API/File_System...

As for (1) vs (2), it’s not really an issue of JavaScript at all. The main question is, do you want to build something that runs in a browser? If you’re building a web app, you’ll have to use the sandboxed APIs (and probably JavaScript). If you don’t care about the runtime, yeah, you can use Node or Bun or Deno (or use another language altogether).