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/agent-tools/matrix.md

@@ -149,7 +149,7 @@ pending invites, resolve_invite to accept or reject`. The daemon clears
 the keyed todo when a `resolve_invite` (or `join_room`) call resolves
 the invite.
 
-See [`docs/2-handbook/integrations/matrix.md`](../../2-handbook/integrations/matrix.md) for the homeserver setup,
+See [`docs/2-handbook/swarm/matrix.md`](../../2-handbook/swarm/matrix.md) for the homeserver setup,
 provisioning flow, and federation config.
 
 ## Extra MCP servers (per-agent)