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.

sops/machines/phantom-ship/key.json

@@ -0,0 +1,6 @@
+[
+  {
+    "publickey": "age18gtjh28qxeltg2r2tzxwl096crkqkqk8tjhersyf7mzdsddady7qs34x0m",
+    "type": "age"
+  }
+]

sops/machines/sunken-ship/key.json

@@ -0,0 +1,6 @@
+[
+  {
+    "publickey": "age1zy3q73pujauyajgfqwu0pnyy8732lzwvw87tu7p2xg3xuzaujc2qh6ql77",
+    "type": "age"
+  }
+]