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.

hive-agent/src/main.rs

@@ -4,7 +4,7 @@
 //! generic and testable. Sibling: `hive-agent-mcp` (the MCP server this
 //! loop points claude at).
 //! Architecture lives in
-//! `docs/turn-loop/::Harness binary shape`.
+//! `docs/4-implementation/turn-loop/::Harness binary shape`.
 //!
 //! Single bin crate: the module tree below (formerly this crate's `lib.rs`,
 //! before lib + bin were collapsed into one) plus the serve loop.
@@ -469,7 +469,7 @@ fn spawn_todo_socket(
 /// Boot — wires up the web UI, login state, stats, plugins, forge
 /// notifier, and either drops into `serve_loop` directly (`Online`) or
 /// parks on the login flow first (`NeedsLogin`). See
-/// `docs/turn-loop/README.md::Boot wiring`.
+/// `docs/4-implementation/turn-loop/README.md::Boot wiring`.
 async fn serve_main<S: Surface>(socket: &Path, poll_ms: u64) -> Result<()> {
     let port = std::env::var("HIVE_PORT")
         .ok()