Thanks for the read!

I think the bookmark idea would work as long as it keeps things at the correct depth. You could also use symlinks for this too which would make the integration with the terminal work well.

I'd imagine instead of having the bookmarks at the ID level (47.01, 47.02 etc) maybe a level lower would work better so you can have:

- 47 Projects

- - 47.01 Project A

- - - code (symlink to code checked out elsewhere)

- - - relevant file 1

- - - relevant file 2

That way you've got access to the code next to the files relating to it.

I'm mostly using Johnny Decimal for non-code files so I can sync them between machines so symlinks would break between OS' which is why I just didn't bother with code, however might work for you use case.