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.

docs/4-implementation/turn-loop/claude-invocation.md

@@ -216,7 +216,7 @@ agent's durable bind-mounted dir. AGENTS.md autoload walks
 upward from `/state` — drop a per-agent AGENTS.md there if you
 want long-term hints that survive destroy/recreate. A `CLAUDE.md`
 in `/state` or above it shadows `AGENTS.md`: claude then loads only
-the `CLAUDE.md` (see `docs/2-handbook/agent-lifecycle/persistence.md` for the
+the `CLAUDE.md` (see `docs/2-handbook/agents/persistence.md` for the
 boot-time rename).
 
 The wake prompt is intentionally minimal: the popped message's