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/agents/README.md

@@ -0,0 +1,24 @@
+# Agents
+
+An **agent** is one Claude instance in its own NixOS container, with its own
+state directory, forge account and matrix accounts. This section covers
+running one: its identity, what survives a restart, how its config changes, what
+its own page shows and how far you can trust it.
+
+- **[Roster](agent-roster.md)** — the agents of a hive, and who may do what
+  to whom.
+- **[Persistence](persistence.md)** — what survives a restart, a destroy and
+  a purge.
+- **[Config changes](config-changes.md)** — how a change to an agent's config
+  flows from a pull request to its container.
+- **[The agent's web page](web-page.md)** — the per-agent terminal view, its
+  actions and its endpoints.
+- **[Security model](security.md)** — the trust model, the prompt-injection
+  threat model and credential isolation.
+
+The swarm creates and configures agents: the create form and its archetypes
+are in [`swarm/archetypes.md`](../swarm/archetypes.md), logging an agent in to
+claude is in [`swarm/claude-login.md`](../swarm/claude-login.md), and you set
+an agent's permissions with `swarmctl agent permissions` or on the swarm UI.
+What an agent can do inside its container is in
+[`4-implementation/agent-tools/`](../../4-implementation/agent-tools/README.md).