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.

frontend/packages/agent/src/screen.html

@@ -36,7 +36,7 @@
     <script>
       // Minimal RFB-over-WebSocket renderer. Connects to `screen/ws` on
       // the same host; the harness relays raw RFB bytes to the VNC server
-      // running inside the container. See docs/web-ui/agent.md (GET /screen)
+      // running inside the container. See docs/2-handbook/web-ui/agent.md (GET /screen)
       // for the design rationale + canvas-sizing implementation notes.
 
       (function () {
@@ -61,7 +61,7 @@
         });
 
         // --- Fit-to-window toggle ---
-        // See docs/web-ui/agent.md::Per-agent endpoints (GET /screen) for the
+        // See docs/2-handbook/web-ui/agent.md::Per-agent endpoints (GET /screen) for the
         // localStorage persistence + canvas-intrinsic-resolution +
         // pointer-rescale model.
         let fitMode = localStorage.getItem("screen-fit") !== "off";
@@ -105,7 +105,7 @@
         // Sends an RFB SetDesktopSize request so the VNC server (weston)
         // changes its actual output resolution to match the browser
         // viewport — sharper than fit-mode's CSS downscale. Gated on the
-        // server's ExtendedDesktopSize advert; see docs/web-ui/agent.md::Per-agent
+        // server's ExtendedDesktopSize advert; see docs/2-handbook/web-ui/agent.md::Per-agent
         // endpoints (GET /screen).
         let extDesktopSupported = false;
         let screenId = 1; // captured from the server's ExtendedDesktopSize advert