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/shared/src/badge/Badge.tsx

@@ -17,7 +17,7 @@
 // them with no real distinction to justify it. Lives in `shared` because both
 // swarm-ui *and* the per-agent page need the interactive shape, and
 // `shared` is the one package both already depend on (see
-// `docs/web-ui/design-guide.md`'s component-first + junk-drawer rules).
+// `docs/5-project/web-ui/design-guide.md`'s component-first + junk-drawer rules).
 import type { ComponentChildren } from "preact";
 import "./Badge.css";