docs: sort the top-level directories into five sections by what the reader wants

Every docs directory moves under 1-getting-started, 2-handbook,
4-implementation or 5-project; the options reference (section 3) comes from
the website and has no directory here. trust-boundary stays whole under the
handbook for now. web-ui, swarm and tools split between handbook and
implementation, and the command-line references move to
2-handbook/reference. Links, path references in code and nix, and the docs
index follow the moves; no page content changes.

hive-c0re/src/stats/container_stats.rs

@@ -13,7 +13,7 @@
 //! No network: agents share the host network namespace
 //! (`privateNetwork = false`), so there is no per-container net
 //! counter to read. Per-agent network only becomes meaningful with the
-//! netns-isolation roadmap (`docs/networking/network.md`).
+//! netns-isolation roadmap (`docs/4-implementation/networking/network.md`).
 //!
 //! CPU is cumulative (`usage_usec` is monotonic), so a single read is
 //! meaningless — we sample every machine's counter, sleep one short

hive-c0re/src/stats/host_stats.rs

@@ -12,7 +12,7 @@
 //!
 //! The registry has no dashboard banner any more. A raised warning reaches
 //! the operator as the `hyperhive.hive.warning` gauge and a Grafana alert
-//! on it (see `docs/scheduler/observability.md`).
+//! on it (see `docs/4-implementation/scheduler/observability.md`).
 
 use serde::Serialize;
 use utoipa::ToSchema;