docs: the handbook follows the three layers: swarm, hives, agents

The handbook's sections were agent-lifecycle, integrations, swarm, tools,
trust-boundary and web-ui, which do not follow how the system is built, so a
reader could not tell which layer a page is about. Its pages now sit in
swarm/, hives/ and agents/, with the accounts an agent can hold outside the
system in external-accounts/.

- swarm/: forge, matrix and the knowledge repo join the swarm pages, and so
  does the swarmctl reference.
- hives/: the dashboard, hivectl and its reference, and the operator/agent
  boundary, with a README that takes over the old web-ui and tools pages.
- agents/: the roster, persistence, config changes, the agent's own web page
  (was web-ui/agent) and the security model, with a README.
- external-accounts/: GitHub and GitLab.

Pages are moved whole; none is split yet. Every reference follows: relative
links in the docs, `docs/2-handbook/...` paths in code comments, the nix
checks that regenerate the CLI references and the ignore list, and docs/README.md,
whose handbook section is now by layer.

nix/agent-modules/weston-vnc.nix

@@ -38,7 +38,7 @@ in
   # Port allocation, weston bind-address quirk, PAM service name, the
   # Type=simple choice, idle-time=0: all in
   # docs/5-project/process/gotchas.md::Weston VNC compositor.
-  # Harness-side WebSocket relay shape: docs/2-handbook/web-ui/agent.md::Per-agent
+  # Harness-side WebSocket relay shape: docs/2-handbook/agents/web-page.md::Per-agent
   # endpoints (`/screen` + `/screen/ws`).
 
   options.services.hyperhive.agent.gui.enable = lib.mkOption {