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/scheduler/observability.md

@@ -104,7 +104,7 @@ smuggled out in resource attributes on an otherwise-legitimate export.
 That's a **different risk from the one the collector fixes**: an agent that
 held the upstream credential could do everything above _and_ use the token
 anywhere else. The collector removes the token and keeps the pipe. Agents are inside the trust
-boundary (`docs/2-handbook/trust-boundary/security.md`: capability = accepted risk), so an agent being
+boundary (`docs/2-handbook/agents/security.md`: capability = accepted risk), so an agent being
 able to _send_ is an accepted extension of that boundary — but it's not
 closed by this design, and don't read anything here as closing it.