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-host-sock/README.md

@@ -25,6 +25,6 @@ needs (`State`, `NodeId`) is protocol-local. The typed
 served as a generic graph (`hive-jobq-wire`), not as a second hand-written
 view.
 
-See `docs/2-handbook/trust-boundary/boundary.md` (host admin socket access) for the trust model around who
+See `docs/2-handbook/hives/boundary.md` (host admin socket access) for the trust model around who
 may connect to the socket, and `hive-priv-sock` for the sibling split on the
 privileged-helper socket.

hive-host-sock/src/lib.rs

@@ -90,7 +90,7 @@ pub enum HostRequest {
     /// `Kill`.
     Kill { name: Ident },
     /// Tear down a sub-agent container, optionally purging state.
-    /// See `docs/2-handbook/agent-lifecycle/config-changes.md::Destroy semantics`.
+    /// See `docs/2-handbook/agents/config-changes.md::Destroy semantics`.
     Destroy {
         name: Ident,
         #[serde(default)]