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/paths.rs

@@ -7,7 +7,7 @@
 //! Claude credentials live at `$HOME/.claude` (resolves to
 //! `/home/<agent-name>/.claude` because the harness service runs as a
 //! non-root unix user matching the agent label — see
-//! `docs/2-handbook/agent-lifecycle/persistence.md::First-boot agent-user migration`).
+//! `docs/2-handbook/agents/persistence.md::First-boot agent-user migration`).
 //!
 //! All three paths can be overridden via env vars (`HYPERHIVE_STATE_DIR`,
 //! `HYPERHIVE_HARNESS_DIR`, `HYPERHIVE_CLAUDE_DIR`) for dev / test scenarios.