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-agent/src/harness_state.rs

@@ -88,7 +88,7 @@ fn effort_from(configured: Option<&str>, file: Option<String>) -> (String, Sourc
 // (`hyperhive-rate-limited`, `hyperhive-needs-login`) that grew organically
 // and had no shared schema. A single JSON file is self-documenting, atomic
 // to write, and cheaper for hive-c0re to read on each sweep (one fopen vs
-// two stat calls). See `docs/2-handbook/agent-lifecycle/persistence.md::Harness state files`.
+// two stat calls). See `docs/2-handbook/agents/persistence.md::Harness state files`.
 //
 // Legacy sentinel files written by older harness builds are still honoured
 // by `read_harness_state` so in-place upgrades don't lose state (the new