Remove CommandEnv::apply
It's not being used and uses unsound set_var and remove_var functions. This is an internal function that isn't exported (even with `process_internals` feature), so this shouldn't break anything.
Also see #92365. Note that this isn't the only use of those methods in standard library, so that particular pull request will need more changes than just this to work (in particular, `test_capture_env_at_spawn` is using `set_var` and `remove_var`).