I think you are on the right track but the solution is not to shrug shoulders.
We should acknowledge there are serious problems with the interface, list them,
and try to fix them. One example is `git add $tracked_file` being wrong, it
should be `git stage $tracked_file`.

I agree. The "stage area" is a very important concept in git, why not
talk git commands that refers to it? Then we could add flags like
--new-files or --deleted-files for better granularity than the current
--all flag.

The real problem is that the core developers of Git don't acknowledge these
user-interface issues, according the them the interface doesn't require any
major changes. Which goes contrary to what most of the world believes.

I think most people agree with these interfaces issues but it's a hard
problem to solve, so  they are reluctant to talk about it because they
fear the can of worm. If someone came with a good solution most people
would be willing to consider it.

I think starting by documenting the issues is a good idea, maybe on a
wiki, and start some draft of a proposed solution that would improve
in an iterative process.

Philippe