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/swarm/inference.md

@@ -30,7 +30,7 @@ swarmctl agent inference clear iris
   running on, each with where it comes from.
 - `clear` removes every field; the agent goes back to its own values.
 
-The full flag reference is [`swarmctl-cli.md`](../../2-handbook/tools/swarmctl-cli.md). The
+The full flag reference is [`swarmctl-cli.md`](../../2-handbook/swarm/swarmctl-cli.md). The
 swarm UI's agents page edits the same settings; see [UI](../../2-handbook/swarm/ui.md). The
 swarm is the only place to change an agent's model or effort at runtime:
 its web UI shows both but has no picker and no `/model` or `/effort`