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.

docs/4-implementation/crates/README.md

@@ -0,0 +1,13 @@
+# Crate reference
+
+One page per Rust workspace crate — its own `README.md`, unchanged, served
+here for browsing alongside the rest of the docs site. **The crate's own
+`README.md` is the source of truth; nothing here is hand-maintained.**
+`nix/packages/reference-docs.nix` generates every page at
+build time straight from the crate's real `README.md`, so it can never
+drift out of sync the way a hand-copied mirror would — edit the crate's
+own README to change what shows up here.
+
+For the one-line-per-crate index (which crate does what, at a glance)
+see the main [`AGENTS.md`](../../../AGENTS.md#repo-map) repo map instead;
+this section is each crate's own, longer word on itself.