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/matrix.nix

@@ -302,7 +302,7 @@ in
     # Long-running matrix-sdk client + sync per agent. Serves the MCP
     # tools directly over streamable-http + emits hyperhive wake
     # signals on incoming room events via `/run/hive/mcp.sock`. See
-    # `docs/2-handbook/agent-lifecycle/persistence.md::Matrix per-agent daemon + token-arrival
+    # `docs/2-handbook/agents/persistence.md::Matrix per-agent daemon + token-arrival
     # trigger` for the first-boot-ordering rationale.
     systemd.services.hive-matrix-daemon = lib.mkIf matrixEnabled {
       description = "long-running matrix-sdk Client + MCP daemon";
@@ -434,7 +434,7 @@ in
     # `tokenFile`, or a `main` from before the swarm minted it). Without this
     # the daemon would exit 0 silently on first boot and the MCP
     # would have no backend until next restart. See
-    # `docs/2-handbook/agent-lifecycle/persistence.md` (same section as above).
+    # `docs/2-handbook/agents/persistence.md` (same section as above).
     systemd.paths.hive-matrix-daemon = lib.mkIf matrixEnabled {
       description = "trigger hive-matrix-daemon when a matrix token appears";
       wantedBy = [ "multi-user.target" ];