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.
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@ -79,7 +79,7 @@ pub(super) async fn post_login_cancel(State(state): State<AppState>) -> Response
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/// The turn loop's next iteration parks into `wait_for_login` which
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/// resumes when a fresh credentials file appears via `/login/code`.
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/// Always returns 200 with a body describing what happened. See
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/// `docs/web-ui/agent.md::Per-agent endpoints`
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/// `docs/2-handbook/web-ui/agent.md::Per-agent endpoints`
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/// (the `/api/logout` bullet) for the three-step rationale +
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/// preservation invariants.
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pub(super) async fn post_logout(State(state): State<AppState>) -> Response {
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