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/README.md

@@ -27,7 +27,7 @@ agents) runs:
    queued and unacked, so a resume drains the backlog instead of
    losing it; reminders and todo wakes buffer in their channels. Set
    it with `hivectl agent <name> pause` or the dashboard toggle; see
-   [persistence](../../2-handbook/agent-lifecycle/persistence.md#-harnesspaused-per-agent).
+   [persistence](../../2-handbook/agents/persistence.md#-harnesspaused-per-agent).
 1. Long-poll `Recv` on its socket. The host-side broker
    (`broker.rs::recv_blocking_batch`) returns immediately if there's
    a pending message, otherwise waits up to 30 s for a broker `Sent`
@@ -118,14 +118,14 @@ installs claude plugins, spawns `web_ui::serve` + `vacuum::run`,
 and either drops into `serve_loop` directly (`Online`) or parks on
 the login flow first (`NeedsLogin`). `hive-forge-notify` polls forge
 notifications on its own, not this loop — see
-[`forge.md`](../../2-handbook/integrations/forge.md).
+[`forge.md`](../../2-handbook/swarm/forge.md).
 
 Boot also opens the todos store and the socket in-container producers
 dial. Matrix / bash / forge-notify daemons and the in-process
 `disk_watch` todo producer (low state-disk space) are the built-in
 producers, but the socket accepts any `subsystem` marker — a
 user-configured MCP server can push its own todos the same way. See
-[`docs/2-handbook/agent-lifecycle/persistence.md`](../../2-handbook/agent-lifecycle/persistence.md#state-dirs-per-agent) for
+[`docs/2-handbook/agents/persistence.md`](../../2-handbook/agents/persistence.md#state-dirs-per-agent) for
 what each built-in todo producer watches and how the store + `get_loose_ends`
 merge work.