@Minijackson thanks for the support/effort :)

warning: Git tree '/home/tom/.dotfiles' is dirty
Resolved URL:  git+file:///home/tom/.dotfiles
Locked URL:    git+file:///home/tom/.dotfiles
Description:   System Flake
Path:          /nix/store/qsnjxr9bf9kki8pd1h8whl8z98i2h406-source
Last modified: 2023-04-23 22:06:25
Inputs:
├───home-manager: github:nix-community/home-manager/3144311f31194b537808ae6848f86f3dbf977d59
│   └───nixpkgs: github:nixos/nixpkgs/645bc49f34fa8eff95479f0345ff57e55b53437e
└───nixpkgs: github:NixOS/nixpkgs/937a9d1ee7b1351d8c55fff6611a8edf6e7c1c37

building Nix...
building the system configuration...
mkdir /run/nixos: Permission denied at /nix/store/aljw17f9h225ygszigg82cpnxhf5cmws-nixos-system-nixos-22.11.3955.7449971a3ec/bin/switch-to-configuration line 91.
warning: error(s) occurred while switching to the new configuration

warning: Git tree '/home/tom/.dotfiles' is dirty
building the system configuration...
warning: Git tree '/home/tom/.dotfiles' is dirty
Warning: The unit file, source configuration file or drop-ins of local-fs.target changed on disk. Run 'systemctl daemon-reload' to reload units.
Warning: The unit file, source configuration file or drop-ins of remote-fs.target changed on disk. Run 'systemctl daemon-reload' to reload units.
activating the configuration...
setting up /etc...
restarting systemd...
reloading user units for tom...
setting up tmpfiles
the following new units were started: docker.service, docker.socket

hmm, it contains

[Unit]
Description=PipeWire PulseAudio
ConditionUser=!root
Conflicts=pulseaudio.socket

[Socket]
Priority=6
ListenStream=%t/pulse/native

[Install]
WantedBy=sockets.target

That's the same as in the built result

I have a bin/update script in my flake repo that has this:

#!/usr/bin/env bash
set -e

echo "> sudo nix-channel --update"
sudo nix-channel --add https://github.com/nix-community/home-manager/archive/master.tar.gz home-manager
sudo nix-channel --update

echo "> nix-env -u --always"
nix-env -u --always

echo "> nix flake update"
nix --extra-experimental-features nix-command --extra-experimental-features flakes flake update

echo "> sudo nixos-rebuild build --flake '.#drakkar' --show-trace"
sudo nixos-rebuild build --flake '.#drakkar' --show-trace
echo "> sudo ./result/activate"
sudo ./result/activate
echo "> rm -f ./result"
rm -f ./result

echo "> home-manager switch --flake '.' --show-trace"
home-manager switch --flake '.' --show-trace

echo "> nixos-generate-config --show-hardware-config > hosts/drakkar/hardware-configuration.nix"
nixos-generate-config --show-hardware-config > hosts/drakkar/hardware-configuration.nix

I run that whenever I make changes to the config and also to update packages. It should build the flake file and not the /etc/nixos/configuration.nix right?