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.

hivectl/README.md

@@ -30,4 +30,4 @@ dispatch:
 - **`quota.rs`**, **`util.rs`**, **`completions.rs`** — shared helpers
   and shell completions.
 
-Full verb reference: `docs/2-handbook/tools/hivectl.md`.
+Full verb reference: `docs/2-handbook/hives/hivectl.md`.

hivectl/src/choom.rs

@@ -79,7 +79,7 @@ fn require_privilege() -> Result<()> {
 /// Execs `machinectl shell <name>@h-<name>` running claude as the agent
 /// user from its state dir, reproducing the harness's per-turn claude
 /// invocation (flags, session selection, why it never collides with the
-/// live harness session). See `docs/2-handbook/tools/hivectl.md` (Choom) for the
+/// live harness session). See `docs/2-handbook/hives/hivectl.md` (Choom) for the
 /// full rationale. Inherits the caller's PTY; requires root or `hive-admin`
 /// group membership, plus a running container.
 ///