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/agent-service.nix

@@ -189,7 +189,7 @@ in
       not `state/` — `harness/` survives container rebuilds exactly like
       `state/` does, but is never bind-mounted into another agent's
       container (unlike `state/`, which a `ManageRootAgent` holder gets
-      read-write for recovery — see `docs/2-handbook/agent-lifecycle/persistence.md`'s "Cross-agent access to
+      read-write for recovery — see `docs/2-handbook/agents/persistence.md`'s "Cross-agent access to
       state"), so this credential is reachable by nothing but this agent
       and the host. Permissions should be `0600`, owned by the agent's
       unix user. Whatever owner it was installed with, the file becomes