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/harness_state.rs

@@ -88,7 +88,7 @@ fn effort_from(configured: Option<&str>, file: Option<String>) -> (String, Sourc
 // (`hyperhive-rate-limited`, `hyperhive-needs-login`) that grew organically
 // and had no shared schema. A single JSON file is self-documenting, atomic
 // to write, and cheaper for hive-c0re to read on each sweep (one fopen vs
-// two stat calls). See `docs/2-handbook/agent-lifecycle/persistence.md::Harness state files`.
+// two stat calls). See `docs/2-handbook/agents/persistence.md::Harness state files`.
 //
 // Legacy sentinel files written by older harness builds are still honoured
 // by `read_harness_state` so in-place upgrades don't lose state (the new

hive-agent/src/login.rs

@@ -33,7 +33,7 @@ pub fn default_dir() -> PathBuf {
 /// exactly these to force re-login while preserving session-history files —
 /// so boot detection ([`has_session`]) and logout agree by construction.
 /// Rationale + the previous wholesale-wipe shape we replaced live in
-/// `docs/2-handbook/web-ui/agent.md::Per-agent endpoints`
+/// `docs/2-handbook/agents/web-page.md::Per-agent endpoints`
 /// (the `/api/logout` bullet).
 ///
 /// `.credentials.json` is the actual OAuth session; `mcp-needs-auth-cache.json`

hive-agent/src/paths.rs

@@ -7,7 +7,7 @@
 //! Claude credentials live at `$HOME/.claude` (resolves to
 //! `/home/<agent-name>/.claude` because the harness service runs as a
 //! non-root unix user matching the agent label — see
-//! `docs/2-handbook/agent-lifecycle/persistence.md::First-boot agent-user migration`).
+//! `docs/2-handbook/agents/persistence.md::First-boot agent-user migration`).
 //!
 //! All three paths can be overridden via env vars (`HYPERHIVE_STATE_DIR`,
 //! `HYPERHIVE_HARNESS_DIR`, `HYPERHIVE_CLAUDE_DIR`) for dev / test scenarios.

hive-agent/src/vacuum.rs

@@ -11,7 +11,7 @@
 //! Trade-off (accepted — issue tracker "perms borked"): a misbehaving harness
 //! could skip its own cleanup, which the host-side version was meant to
 //! prevent. But a compromised harness is already inside the container trust
-//! boundary (`docs/2-handbook/trust-boundary/security.md`), and these are ephemeral local artifacts — so
+//! boundary (`docs/2-handbook/agents/security.md`), and these are ephemeral local artifacts — so
 //! the honest fix is to clean them up where they live.
 
 use std::path::Path;

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: