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/base.css

@@ -2,7 +2,7 @@
    web UI. The colour variables it references (`--bg`, `--fg`, …) live in
    the standalone `theme.css` (Catppuccin Mocha), linked separately by
    every page BEFORE this file so the `:root` vars resolve — see
-   `theme.css` + docs/web-ui/css-vars.md. Per-page stylesheets append on
+   `theme.css` + docs/4-implementation/web-ui/css-vars.md. Per-page stylesheets append on
    top of this and must NOT redeclare the colour variables; `theme.css`
    is the one source of truth. */
 body {