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/trust-boundary/boundary-mechanism.md

@@ -2,7 +2,7 @@
 
 How systemd activates `hive-priv` and how the per-agent socket directory
 gets its owner and mode, the two pieces of the boundary described in
-[the operator/agent boundary](../../2-handbook/trust-boundary/boundary.md).
+[the operator/agent boundary](../../2-handbook/hives/boundary.md).
 
 ## hive-priv socket activation
 
@@ -42,7 +42,7 @@ root:root`, no symlink followed) and leaves an existing one alone. The
 container's own activation (`hive-agent-user-migrate`) then chowns it to
 the agent user and sets `0751`. Without a user namespace
 that uid is the host inode's owner. (A namespaced agent, see "User namespace" in
-`docs/2-handbook/agent-lifecycle/persistence.md`, gets the dir from `EnsureAgentSocketDir`
+`docs/2-handbook/agents/persistence.md`, gets the dir from `EnsureAgentSocketDir`
 owned by its data owner instead, because the container can't chown through
 the id map.) Don't add another host-side chown or chmod:
 two owners of one path revert each other. Until the container activates,

docs/4-implementation/trust-boundary/hive-c0re-privilege.md

@@ -1,7 +1,7 @@
 # hive-c0re privilege separation
 
 How `hive-c0re` runs unprivileged and delegates its root operations to
-`hive-priv`, from the [security model](../../2-handbook/trust-boundary/security.md).
+`hive-priv`, from the [security model](../../2-handbook/agents/security.md).
 
 ## Background
 

docs/4-implementation/trust-boundary/nix-builds.md

@@ -1,7 +1,7 @@
 # Nix builds and credential isolation
 
 The mechanism and threat model for `nix build` inside an agent container, from
-the [security model](../../2-handbook/trust-boundary/security.md).
+the [security model](../../2-handbook/agents/security.md).
 
 ## Background