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.

nix/archetypes/default.nix

@@ -4,7 +4,7 @@
 # builder evaluates `meta` alone and swarm-controller stores it as JSON.
 # `meta` fields: `description` (required), `permissions`, `limits`,
 # `inference`, in the shapes `POST /api/agents` takes them; see
-# docs/swarm/archetypes.md.
+# docs/2-handbook/swarm/archetypes.md.
 {
   reviewer = {
     module = { };