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/5-project/process/conventions.md

@@ -433,7 +433,7 @@ into the `Swap` node, then runs `nixos-container update` + stop +
 start across the `StopForUpdate → Swap → RebuildBookkeeping`
 brace and the tail `Reconcile` node. `flake.nix` itself lives in the agent's
 `agent-configs/<name>` repo and rides along with its pinned commit (see
-`docs/2-handbook/agent-lifecycle/config-changes.md::Deploy markers per agent`).
+`docs/2-handbook/agents/config-changes.md::Deploy markers per agent`).
 
 Anything that changes per-container state on the host should be
 re-applied here so a manual `↻ R3BU1LD` from the dashboard is
@@ -497,20 +497,20 @@ mara — don't add `#[allow]` speculatively. The gate is intentional.
 fmt / `cargo test` cover most gates, but `nix flake check` runs extra
 check derivations they don't:
 
-- **`hivectl-docs`** regenerates `docs/2-handbook/tools/hivectl-cli.md` from
+- **`hivectl-docs`** regenerates `docs/2-handbook/hives/hivectl-cli.md` from
   hivectl's clap tree and **fails if the committed copy is stale**.
   **After any change to a hivectl verb or flag, regenerate it**:
   ```sh
-  nix develop -c cargo run --bin hivectl -- markdown-docs > docs/2-handbook/tools/hivectl-cli.md
+  nix develop -c cargo run --bin hivectl -- markdown-docs > docs/2-handbook/hives/hivectl-cli.md
   ```
   clippy / fmt / `cargo test` all pass *without* this — only the
   flake check catches the drift, and `ci-log` often can't show you
   why (it 500s on a fast failure), so you're left guessing "builder
   flake" when it's a stale doc.
 - **`swarmctl-docs`** is the same check for `swarmctl` /
-  `docs/2-handbook/tools/swarmctl-cli.md`:
+  `docs/2-handbook/swarm/swarmctl-cli.md`:
   ```sh
-  nix develop -c cargo run --bin swarmctl -- markdown-docs > docs/2-handbook/tools/swarmctl-cli.md
+  nix develop -c cargo run --bin swarmctl -- markdown-docs > docs/2-handbook/swarm/swarmctl-cli.md
   ```
 - there's also a flake `cargo-test` check and NixOS module
   evaluation in the set.
@@ -554,7 +554,7 @@ provisioning time:
 
 (The matrix profile avatar is **not** a oneshot — `hive-matrix-daemon`
 sets it over its live authenticated Client; see
-`docs/2-handbook/agent-lifecycle/persistence.md::matrix avatar`.)
+`docs/2-handbook/agents/persistence.md::matrix avatar`.)
 
 Shape contract — every one of these:
 
@@ -575,7 +575,7 @@ Shape contract — every one of these:
 5. **Re-runnable**: a second invocation produces the same final
    state (idempotent uploads, idempotent config rewrites). Used
    by the `.path` watchers that re-fire on token appearance (see
-   `docs/2-handbook/agent-lifecycle/persistence.md::Matrix per-agent daemon`).
+   `docs/2-handbook/agents/persistence.md::Matrix per-agent daemon`).
 
 The service stays root-owned so the bootstrap ordering doesn't need a
 user-existence check before each fire.

docs/5-project/process/gotchas.md

@@ -205,7 +205,7 @@ durable knowledge here (`notes.md`, anything else) — the harness's own
 internal files (`hyperhive-events.sqlite`, `hyperhive-turn-stats.sqlite`,
 `hyperhive-model`) live in the separate `harness` dir instead, so they
 don't clutter what claude sees as "my notes dir" (see
-[`docs/2-handbook/agent-lifecycle/persistence.md`](../../2-handbook/agent-lifecycle/persistence.md)). Survives `destroy`/recreate
+[`docs/2-handbook/agents/persistence.md`](../../2-handbook/agents/persistence.md)). Survives `destroy`/recreate
 alongside the claude dir.
 
 ### Persistent work dir per agent
@@ -336,7 +336,7 @@ nix develop -c cargo run -p hive-c0re --bin hivectl -- <args>
 ```
 
 This is also how you regenerate committed generated docs locally —
-for example `docs/2-handbook/tools/hivectl-cli.md` via the `hivectl markdown-docs`
+for example `docs/2-handbook/hives/hivectl-cli.md` via the `hivectl markdown-docs`
 subcommand (its `hivectl-docs` flake check otherwise only fails in
 CI on drift).
 
@@ -402,7 +402,7 @@ Never use raw `curl` for forge access.
 `nix/agent-modules/weston-vnc.nix` adds an optional Weston Wayland
 compositor with the `vnc-backend` plugin, surfaced as
 `services.hyperhive.agent.gui.enable = true` per-agent. The harness's
-`/screen/ws` WebSocket relay (`docs/2-handbook/web-ui/agent.md::Per-agent endpoints`)
+`/screen/ws` WebSocket relay (`docs/2-handbook/agents/web-page.md::Per-agent endpoints`)
 connects to the compositor at `127.0.0.1:<vnc_port>`.
 
 - **Port allocation**: a **fixed** port (`services.hyperhive.agent.gui.vncPort`,