nixos/etc: switching configuration with `etc.overlay` breaks cwd

[Majiir]

Nixpkgs version

• Stable (25.11)

Describe the bug

When the current working directory is in /etc and you switch to a new configuration that remounts /etc (with etc.overlay), some applications break because getcwd returns an error.

Steps to reproduce

1. cd somewhere in /etc
2. nixos-rebuild test to a config that changes /etc so it remounts
3. python -c 'import os; print(os.getcwd())'

For a real application that breaks, try jj.

Expected behaviour

Switching configuration should not break an open directory that is present in both the old and new /etc.

Screenshots

No response

Relevant log output

[nix-shell:/etc/nixos]$ pwd
/etc/nixos

[nix-shell:/etc/nixos]$ echo $PWD
/etc/nixos

[nix-shell:/etc/nixos]$ python -c 'import os; print(os.getcwd())'
/etc/nixos

[nix-shell:/etc/nixos]$ nixos-rebuild test --sudo
building the system configuration...
activating the configuration...
remounting /etc...
Moving mount
Mounting beneath top mount
Attaching mount /run/nixos-etc.kQvjgZCHpo -> /etc
Moving single attached mount
reloading user units for majiirpaktu...
restarting sysinit-reactivation.target
the following new units were started: run-keys.mount, run-nixos\x2detc\x2dmetadata.r6kDbokHLZ.mount, sysinit-reactivation.target, systemd-tmpfiles-resetup.service
Done. The new configuration is /nix/store/xy39zvnc2kzif9q2955fvhzbcx79jny2-nixos-system-server-25.11.20251223.76701a1

[nix-shell:/etc/nixos]$ pwd
/etc/nixos

[nix-shell:/etc/nixos]$ echo $PWD
/etc/nixos

[nix-shell:/etc/nixos]$ python -c 'import os; print(os.getcwd())'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import os; print(os.getcwd())
                     ~~~~~~~~~^^
FileNotFoundError: [Errno 2] No such file or directory

[nix-shell:/etc/nixos]$ cd /etc/nixos

[nix-shell:/etc/nixos]$ python -c 'import os; print(os.getcwd())'
/etc/nixos

[nix-shell:/etc/nixos]$ jj
Error: Could not determine current directory
Hint: Did you update to a commit where the directory doesn't exist or can't be accessed?

Additional context

Since we put the config in /etc/nixos by default, it's probably not uncommon that a user would hit this situation.

System metadata

• system: "x86_64-linux"
• host os: Linux 6.12.63, NixOS, 25.11 (Xantusia), 25.11.20251223.76701a1
• multi-user?: yes
• sandbox: yes
• version: nix-env (Nix) 2.31.2

Notify maintainers

@nikstur

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[nikstur]

This is unfortunate but unavoidable because we switch the mount points and thus you are actually in a different directory. You will need to change into /etc again after switching before getcwd() can work again.