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/4-implementation/turn-loop/mcp.md

@@ -144,7 +144,7 @@ hive_name?, swarm_name?, matrix_accounts? }`. `matrix_accounts` is a
   [`docs/4-implementation/agent-tools/subagent.md`](../agent-tools/subagent.md).
 - **Config changes** — no permission: they go through a forge PR on
   `agent-configs/<name>` — see
-  [`docs/2-handbook/agent-lifecycle/config-changes.md`](../../2-handbook/agent-lifecycle/config-changes.md).
+  [`docs/2-handbook/agents/config-changes.md`](../../2-handbook/agents/config-changes.md).
 - **Web egress** (`web_tools`) — enables Claude's built-in `WebFetch`
   and `WebSearch` tools (not MCP tools; added directly to the
   `--allowedTools` list). Off by default.