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/README.md

@@ -27,7 +27,7 @@ agents) runs:
    queued and unacked, so a resume drains the backlog instead of
    losing it; reminders and todo wakes buffer in their channels. Set
    it with `hivectl agent <name> pause` or the dashboard toggle; see
-   [persistence](../../2-handbook/agent-lifecycle/persistence.md#-harnesspaused-per-agent).
+   [persistence](../../2-handbook/agents/persistence.md#-harnesspaused-per-agent).
 1. Long-poll `Recv` on its socket. The host-side broker
    (`broker.rs::recv_blocking_batch`) returns immediately if there's
    a pending message, otherwise waits up to 30 s for a broker `Sent`
@@ -118,14 +118,14 @@ installs claude plugins, spawns `web_ui::serve` + `vacuum::run`,
 and either drops into `serve_loop` directly (`Online`) or parks on
 the login flow first (`NeedsLogin`). `hive-forge-notify` polls forge
 notifications on its own, not this loop — see
-[`forge.md`](../../2-handbook/integrations/forge.md).
+[`forge.md`](../../2-handbook/swarm/forge.md).
 
 Boot also opens the todos store and the socket in-container producers
 dial. Matrix / bash / forge-notify daemons and the in-process
 `disk_watch` todo producer (low state-disk space) are the built-in
 producers, but the socket accepts any `subsystem` marker — a
 user-configured MCP server can push its own todos the same way. See
-[`docs/2-handbook/agent-lifecycle/persistence.md`](../../2-handbook/agent-lifecycle/persistence.md#state-dirs-per-agent) for
+[`docs/2-handbook/agents/persistence.md`](../../2-handbook/agents/persistence.md#state-dirs-per-agent) for
 what each built-in todo producer watches and how the store + `get_loose_ends`
 merge work.
 

docs/4-implementation/turn-loop/claude-invocation.md

@@ -216,7 +216,7 @@ agent's durable bind-mounted dir. AGENTS.md autoload walks
 upward from `/state` — drop a per-agent AGENTS.md there if you
 want long-term hints that survive destroy/recreate. A `CLAUDE.md`
 in `/state` or above it shadows `AGENTS.md`: claude then loads only
-the `CLAUDE.md` (see `docs/2-handbook/agent-lifecycle/persistence.md` for the
+the `CLAUDE.md` (see `docs/2-handbook/agents/persistence.md` for the
 boot-time rename).
 
 The wake prompt is intentionally minimal: the popped message's

docs/4-implementation/turn-loop/config.md

@@ -330,7 +330,7 @@ KEYS
 The file lives in the agent's bind-mounted **harness** dir, not `state/`
 — `harness/` survives container rebuilds exactly like `state/` does, but
 (unlike `state/`) is never bind-mounted into a parent agent's container
-(see `docs/2-handbook/agent-lifecycle/persistence.md`'s "Parent access to child state"), so an API
+(see `docs/2-handbook/agents/persistence.md`'s "Parent access to child state"), so an API
 key placed here is reachable by nothing but this agent and the host. The
 file doesn't stay root-owned, though: the container's activation chowns the
 whole harness dir to the agent, so after the next boot the file is agent-owned

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.