I haven’t seen git update-index --skip-worktree
mentioned yet. You can read about the motivation for this feature in the git scm docs.
I have used it in the past when a professor wanted us to clone repos for assignments that included some opinionated settings for VSCode that I didn’t want to use. Skipping the work tree for that directory allowed me to change or delete the config files without git complaining every time I pushed or pulled or whatever, and the changes I made remained local.
You could set up a couple git aliases to “freeze” and “thaw” your config files on the second drive.
@[email protected]
On this same train of thought: there’s also git sparse-checkout which uses the skip-worktree bit under the hood, and may have an easier interface. I’m not sure though, I haven’t used it yet.