refactor(nix): move flake to repo root 🚚

clan-cli silently ignores the `?dir=` URL parameter when resolving a
flake source, so with the flake at nixos/flake.nix `clan machines
update` fails with "flake.nix does not exist". Move the flake tree up
so the repo root contains flake.nix, flake.lock, flake-modules/, lib/,
modules/, sops/, and vars/. Host-specific NixOS modules stay in
nixos/{hosts,home,fish.nix,neovim.nix,…}; flake-module paths updated
accordingly.

- dotfiles-rebuild flakeRef is now "${dotfilesDir}#<host>" (was
  "${dotfilesDir}/nixos#<host>").
- CLAUDE.md build commands + clan section updated. nixupdate fish alias
  updated. sunken-ship hostsfile comment updated.
- Existing /etc/dotfiles checkouts on the servers will pick up the new
  layout on the next `dotfiles-rebuild` timer tick; the rebuild service
  was pre-updated via rsync so its flakeRef matches before the pull.

Also includes 4b follow-through: zerotier identities are now live on
both servers (sunken-ship=d553a2de33 controller, phantom-ship=6c048abbdc
peer) and IPv6 ping across the ZT mesh works.

modules/dotfiles-rebuild.nix

@@ -0,0 +1,44 @@
+# Shared auto-rebuild-from-git service for homelab hosts.
+#
+# Every 15 min: git fetch origin, fast-forward main, and if there were any
+# new commits run nixos-rebuild switch against `<dotfilesDir>#<host>`.
+#
+# Assumes /etc/dotfiles is an already-cloned checkout of the dotfiles repo.
+{ config, lib, pkgs, ... }:
+let
+  dotfilesDir = "/etc/dotfiles";
+  flakeRef = "${dotfilesDir}#${config.networking.hostName}";
+in {
+  environment.systemPackages = [ pkgs.git ];
+
+  # Trust /etc/dotfiles as root even though it's owned by `danny`.
+  # nix/libgit2 reads safe.directory from /etc/gitconfig; the GIT_CONFIG_*
+  # env vars on the service only affect the git CLI, not nix.
+  programs.git.enable = true;
+  programs.git.config.safe.directory = [ dotfilesDir ];
+
+  systemd.services.dotfiles-rebuild = {
+    description = "Pull dotfiles and run nixos-rebuild if repo changed";
+    path = with pkgs; [ git nix nixos-rebuild ];
+    environment.GIT_CONFIG_COUNT = "1";
+    environment.GIT_CONFIG_KEY_0 = "safe.directory";
+    environment.GIT_CONFIG_VALUE_0 = dotfilesDir;
+    script = ''
+      set -euo pipefail
+      cd ${dotfilesDir}
+      git fetch origin
+      if [ "$(git rev-parse HEAD)" = "$(git rev-parse origin/main)" ]; then
+        exit 0
+      fi
+      git pull origin main
+      exec nixos-rebuild switch --flake ${flakeRef}
+    '';
+    serviceConfig.Type = "oneshot";
+  };
+
+  systemd.timers.dotfiles-rebuild = {
+    wantedBy = [ "timers.target" ];
+    timerConfig.OnCalendar = "*-*-* *:00/15:00";  # every 15 minutes
+    timerConfig.RandomizedDelaySec = "2min";
+  };
+}