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.

docs/2-handbook/swarm/README.md

@@ -39,6 +39,13 @@ grafana, the controller, authelia, …) →
   `admins` only. → [`ui.md`](ui.md)
 - **shared services** — one forge, homeserver, SSO, queue and metrics/logs
   stack, each on whichever host you put it. → [`services.md`](services.md)
+- **forge** — the swarm's Forgejo: per-agent accounts, notifications and the
+  CLI agents use. → [`forge.md`](forge.md)
+- **matrix** — the swarm's homeserver, several accounts per agent, and
+  federation. → [`matrix.md`](matrix.md)
+- **knowledge repo** — the reference docs every agent reads, and how to add
+  one. → [`knowledge.md`](knowledge.md)
+- **`swarmctl`** — the swarm operator's CLI. → [`swarmctl-cli.md`](swarmctl-cli.md)
 - **SSO** — the secrets authelia generates and how each reaches its reader.
   → [`sso.md`](sso.md)
 - **secrets** — the rules a credential follows → [`credentials.md`](credentials.md);
@@ -453,13 +460,13 @@ them, and the notification router, not the controller, decides what they mean.
 A `config-pr` delivery reporting a PR merged into `main` queues a deploy
 of its `merge_commit_sha` on the one hive whose wanted state places the
 agent; with no such hive, or more than one, the controller deploys nothing. See
-[config-changes.md § Config changes](../agent-lifecycle/config-changes.md#config-changes).
+[config-changes.md § Config changes](../agents/config-changes.md#config-changes).
 A merge whose `closed` delivery never arrives deploys nothing either; the
 operator recovers by redelivering that delivery from the forge hook page,
 which re-enters the same handler and re-queues the deploy.
 
 **`internal/knowledge` is on that path.** The controller's is the only
-hook on it ([`knowledge.md`](../integrations/knowledge.md) covers clearing a
+hook on it ([`knowledge.md`](knowledge.md) covers clearing a
 leftover). A webhook has exactly one target URL, so a second registration
 would take delivery away from the first rather than add a recipient.
 
@@ -479,7 +486,7 @@ host also serves the swarm UI vhost — that's what publishes the
 endpoint, and a hook the forge can't reach would collect failed
 deliveries while looking healthy. The controller generates the HMAC
 secret on first start and keeps it
-(see [`docs/2-handbook/agent-lifecycle/persistence.md`](../agent-lifecycle/persistence.md)).
+(see [`docs/2-handbook/agents/persistence.md`](../agents/persistence.md)).
 
 To check it's working, push to `internal/knowledge` and look for
 `webhook: verified delivery` in `journalctl -u swarm-controller`. A
@@ -588,7 +595,7 @@ mechanism.
    added to the public CAs; it holds the store's `pki` root, so a peer whose
    certificate chains to the same root validates. A peer outside this
    swarm's root needs a CA-issued certificate (ACME). Federation firewall
-   and TLS requirements: [`2-handbook/integrations/matrix.md`](../integrations/matrix.md).
+   and TLS requirements: [`2-handbook/swarm/matrix.md`](matrix.md).
 
 3. **WireGuard mesh** (optional) — `deploy.wireguard.enable` reads each
    entry's `wireguardPublicKey`/`wireguardEndpoint`/`wireguardAddress`
@@ -683,7 +690,7 @@ If both hosts are behind NAT, you need a STUN relay or a third host
   swarm's `btrfs receive` endpoint and the `swarm.snapshotStore` option
 - [`5-project/process/conventions.md`](../../5-project/process/conventions.md) § Hive identity —
   env vars, qualified labels
-- [`2-handbook/integrations/matrix.md`](../integrations/matrix.md) — matrix
+- [`2-handbook/swarm/matrix.md`](matrix.md) — matrix
   federation, TLS cert autogeneration, firewall posture
 - [`4-implementation/networking/gateway.md`](../../4-implementation/networking/gateway.md) — nginx vhosts and
   the `.well-known/matrix/` autodiscovery scheme