Stale references to nix + other issues

Here are a couple of issues with the nix component of this guide:
1. The `Build an air-gapped NixOS LiveCD image` part of the guide no longer works after moving `flake.nix` to `nix` subdirectory. Similar issue with the other commands. Adding `?dir=nix` argument to the [flake url](https://nix.dev/manual/nix/2.13/command-ref/new-cli/nix3-flake#url-like-syntax) should solve the problem.
2. The flake lock file is outdated: it contains `drduhConfig` which was removed from the flake inputs.

And other issues noticed while following it:
1. `sudo mkdir /mnt/encrypted-storage` does not work on NixOS as `/mnt` is not created by default.
1. `gpg-agent` needs to be stopped before using `ykman openpgp` commands.
1. Transfer subkeys just doesn't work (`gpg: KEYTOCARD failed: Invalid time` error). What solved was to run the interactive command manually without `--pinentry-mode=loopback`
1. Running `save` after `keytocard` makes it annoying to transfer the keys to multiple yubikeys, as they are removed from gnupg. I had to delete all secret keys form my gnupg and re-import the backups.
It seems to me like the live NixOS image support is slowly being faded out. Is there a particular reason for this?

Anyways, this was a great guide, thank you to all who contributed to it!