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.

swarmctl/README.md

@@ -61,7 +61,7 @@ an error.
 | `SWARMCTL_SWARM`               | the swarm's domain, bare or `https://`: reach the controller there   |
 | `SWARMCTL_CA_FILE`             | a PEM CA to trust beside the system roots, for `SWARMCTL_SWARM`      |
 
-Every verb and flag: [`docs/2-handbook/tools/swarmctl-cli.md`](../docs/2-handbook/tools/swarmctl-cli.md).
+Every verb and flag: [`docs/2-handbook/swarm/swarmctl-cli.md`](../docs/2-handbook/swarm/swarmctl-cli.md).
 The sections below cover why each verb behaves as it does.
 
 ## `user add`