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/components/Header.tsx

@@ -53,7 +53,7 @@ export interface HeaderProps {
    * a variable pill count) grows to fit badges+pills together, keeping
    * the header a stable height even on widescreen. Meta-nav
    * (`<MetaNav>`) lives here too, as a fixed-size trigger, not an
-   * inline link list in the title row (docs/web-ui/agent.md). */
+   * inline link list in the title row (docs/2-handbook/web-ui/agent.md). */
   pills?: ComponentChildren;
 }