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/agent_set.rs

@@ -46,7 +46,7 @@ pub async fn refresh(agents: &[hive_meta_flake::AgentSpec]) -> Result<()> {
     // Every agent binds a unix socket (`HIVE_WEB_SOCKET`); the gateway routes
     // via this map, falling back to a computed TCP loopback port
     // (`lifecycle::agent_web_port`) only while an agent's socket marker is
-    // absent. See `docs/networking/gateway.md::Per-agent unix-socket upstream`.
+    // absent. See `docs/4-implementation/networking/gateway.md::Per-agent unix-socket upstream`.
     if let Err(e) = crate::agent_sockets::write(&agent_names) {
         tracing::warn!(error = ?e, "agent_sockets::write failed (non-fatal)");
     }