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.

nix/agent-modules/user.nix

@@ -229,7 +229,7 @@ in
     # home dir, chowns the bind-mounted state + `~/.claude/`, and
     # (marker-guarded) moves any leftover `/root/.claude` content
     # from the previous root-run shape. See
-    # `docs/2-handbook/agent-lifecycle/persistence.md::First-boot agent-user migration` for the
+    # `docs/2-handbook/agents/persistence.md::First-boot agent-user migration` for the
     # step-by-step rationale; this script implements it.
     system.activationScripts.hive-agent-user-migrate = lib.stringAfter [ "users" "specialfs" ] ''
       homeDir=${lib.escapeShellArg homeDir}