Comment by Hnus

It actually is specific to flakes. Classic nix commands can see untracked files just fine. Flake evaluation behaves differently because of how it decides which "scheme" to use:

> If the directory is part of a Git repository, then the input will be treated as a `git+file:` URL, otherwise it will be treated as a `path:` url;

This is why untracked or unstaged files disappear when using flakes: