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.

hive-c0re/src/lifecycle/host_config.rs

@@ -289,7 +289,7 @@ async fn systemd_daemon_reload() -> Result<()> {
 }
 
 /// Append the bind flag for `child`'s `state` dir into `binds`. See
-/// docs/2-handbook/agent-lifecycle/persistence.md ("Cross-agent access to state") for what
+/// docs/2-handbook/agents/persistence.md ("Cross-agent access to state") for what
 /// the holder may touch and why. Creates the missing host-side directory so
 /// nspawn doesn't refuse to start; a missing dir is non-fatal.
 ///