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.

README.md

@@ -92,13 +92,13 @@ box it gets:
   credentials, and notifications turned into todos. Optional linked
   accounts on other forges, GitLab (`glab` + push), and GitHub (`gh` + push) via
   `services.hyperhive.agent.github.enable`. →
-  [forge](docs/2-handbook/integrations/forge.md) · [gitlab](docs/2-handbook/integrations/gitlab.md) ·
-  [github](docs/2-handbook/integrations/github.md)
+  [forge](docs/2-handbook/swarm/forge.md) · [gitlab](docs/2-handbook/external-accounts/gitlab.md) ·
+  [github](docs/2-handbook/external-accounts/github.md)
 - **matrix** — its own account(s) on the swarm homeserver, as MCP tools. →
   [matrix](docs/4-implementation/agent-tools/matrix.md)
 - **knowledge** — the swarm's shared `internal/knowledge` repo, read-only
   at `/knowledge`, plus hyperhive's own docs in the container. →
-  [knowledge](docs/2-handbook/integrations/knowledge.md)
+  [knowledge](docs/2-handbook/swarm/knowledge.md)
 - **web UI** — a per-agent page behind the gateway: live terminal of the
   turn stream, model / effort switching, cancel.
 - **GUI** (opt-in, `services.hyperhive.agent.gui.enable`) — a Wayland
@@ -175,11 +175,11 @@ once, top to bottom.
   [`docs/2-handbook/swarm/ui.md`](docs/2-handbook/swarm/ui.md)
 - **`swarmctl`** — the swarm's CLI, on the swarm-controller host: create
   agents and mint their identities, manage SSO users, make forge admins.
-  → [reference](docs/2-handbook/tools/swarmctl-cli.md)
+  → [reference](docs/2-handbook/swarm/swarmctl-cli.md)
 - **per-hive** — each hive's dashboard (container state,
   rebuild queue) and `hivectl` for host-level administration and
-  container shells. → [`docs/2-handbook/web-ui/`](docs/2-handbook/web-ui/README.md) ·
-  [hivectl](docs/2-handbook/tools/hivectl.md)
+  container shells. → [`docs/2-handbook/hives/`](docs/2-handbook/hives/README.md) ·
+  [hivectl](docs/2-handbook/hives/hivectl.md)
 
 You are an SSO user too: `swarmctl user add <you> --group admins`, and a
 first login through authelia creates your forge and matrix accounts;
@@ -193,8 +193,8 @@ pick the page for your task rather than reading front to back. Some
 common entry points:
 
 - connecting hives into a swarm → [`2-handbook/swarm/`](docs/2-handbook/swarm/README.md)
-- how config changes flow → [`2-handbook/agent-lifecycle/config-changes.md`](docs/2-handbook/agent-lifecycle/config-changes.md)
-- trust boundary + threat model → [`trust-boundary/`](docs/2-handbook/trust-boundary/boundary.md)
+- how config changes flow → [`2-handbook/agents/config-changes.md`](docs/2-handbook/agents/config-changes.md)
+- trust boundary + threat model → [`hives/boundary.md`](docs/2-handbook/hives/boundary.md), [`agents/security.md`](docs/2-handbook/agents/security.md)
 - what an agent's turn looks like → [`4-implementation/turn-loop/`](docs/4-implementation/turn-loop/README.md)
 - every `services.hyperhive.*` option → [options reference](https://hyperhive.darkest.space/options/)