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.
