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.

hive-forge-notify/src/bin/hive-github-notify/main.rs

@@ -5,7 +5,7 @@
 //!
 //! Takes no arguments. `HYPERHIVE_STATE_DIR` holds the PAT
 //! (`github-token`, fetched from the swarm secret store by
-//! `nix/agent-modules/github-token.nix` — see `docs/2-handbook/integrations/github.md`)
+//! `nix/agent-modules/github-token.nix` — see `docs/2-handbook/external-accounts/github.md`)
 //! and `HIVE_AGENT_SOCKET` is the harness's todo socket.
 //! Having a PAT *is* the opt-in: with no token the poller logs why and
 //! exits 0, so deploying this unit to an agent that never gets one costs a

hive-forge-notify/src/bin/hive-github-notify/source.rs

@@ -13,7 +13,7 @@ use hive_forge_notify::notify::UNREAD_FETCH_LIMIT;
 use hive_forge_notify::source::Source;
 use tracing::{debug, warn};
 
-/// GitHub's REST base. `docs/2-handbook/integrations/github.md` scopes the integration to
+/// GitHub's REST base. `docs/2-handbook/external-accounts/github.md` scopes the integration to
 /// github.com only — the same constraint the `gh` wrapper and the git
 /// credential helper already carry — so this is a constant rather than
 /// another operator-entered URL.