Often you’ll see an error like this,
error: getting status of '/nix/store/vlks3d7fr5ywc923pvqacx2bkzm1782j-source/foo': No such file or directory
This usually means you have not staged this new file/ directory to the Git index. When using Flakes, Nix will not see untracked files/ directories by default. To resolve this, just git add -N the untracked file/ directory.