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.

hive-agent/src/web_ui/auth.rs

@@ -16,7 +16,7 @@ use super::AppState;
 /// resumes when a fresh credentials file appears (the swarm login stores
 /// one and `claude_credentials` installs it).
 /// Always returns 200 with a body describing what happened. See
-/// `docs/2-handbook/web-ui/agent.md::Per-agent endpoints`
+/// `docs/2-handbook/agents/web-page.md::Per-agent endpoints`
 /// (the `/api/logout` bullet) for the three-step rationale +
 /// preservation invariants.
 pub(super) async fn post_logout(State(state): State<AppState>) -> Response {

hive-agent/src/web_ui/state.rs

@@ -145,7 +145,7 @@ pub(super) struct StateSnapshot {
     /// Navigation links for this agent page. Also served via
     /// `DashboardState.links` (`GET /api/dashboard-state`) for the
     /// dashboard card's icon strip. Both are produced by `agent_links()`
-    /// — single source of truth. See [`docs/2-handbook/web-ui/dashboard.md::Container row`]
+    /// — single source of truth. See [`docs/2-handbook/hives/dashboard.md::Container row`]
     /// for the frontend resolver + which links appear in which conditions.
     links: Vec<AgentLink>,
     /// Public URL of the forge (e.g.
@@ -276,7 +276,7 @@ fn read_own_status() -> (Option<String>, Option<i64>) {
 /// for `External`; the frontend resolves each against its `kind`
 /// against the right base so the backend never has to guess the
 /// operator's browser host. See
-/// `docs/2-handbook/web-ui/dashboard.md::Container row` for
+/// `docs/2-handbook/hives/dashboard.md::Container row` for
 /// the resolver + how `deployed:<sha>` ships alongside.
 ///
 /// Icons are real emoji, not unicode arrow/geometric glyphs — mara: