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/index.html

@@ -19,7 +19,7 @@
   <body class="agent-shell">
     <!-- The Preact rewrite owns everything below — header, terminal,
        side panel. See main.tsx/Root.tsx for the component
-       tree; docs/web-ui/agent.md for the design. -->
+       tree; docs/2-handbook/web-ui/agent.md for the design. -->
     <div id="preact-root"></div>
 
     <script type="module" src="static/main.js" defer></script>