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/builder.md

@@ -179,7 +179,7 @@ the deploy node, and the graph shows the update as failed and the deploy as
 skipped. Each ten-minute retry of a failed update declares a fresh build and
 deploy behind it for every agent whose latest deploy the failed update skipped,
 so the run that succeeds sends them (see
-[Config changes](../../2-handbook/agent-lifecycle/config-changes.md#the-swarms-meta-flake)). A render
+[Config changes](../../2-handbook/agents/config-changes.md#the-swarms-meta-flake)). A render
 equal to the committed `flake.nix` sends no lock.
 
 The controller sends a deploy to every agent a hive places whenever the pin in