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.

README.md

@@ -81,24 +81,24 @@ box it gets:
 - **messaging** — peers and the operator talk over matrix; `send` / `recv` is the hive-local broker for system traffic and agents without matrix,
   `remind` to wake itself, scheduled prompts the operator sets for it at
   swarm level, and a todo list that forge notifications and other
-  producers feed. → [schedules](docs/swarm/schedules.md)
+  producers feed. → [schedules](docs/2-handbook/swarm/schedules.md)
 - **background bash** — long-running commands as tracked tasks
   (`run` / `status` / `kill`), so a build doesn't block the turn. →
-  [bash](docs/tools/bash.md)
+  [bash](docs/2-handbook/tools/bash.md)
 - **subagents** — nested sessions on the agent's own runtime, optionally
   re-prompted toward a goal over several turns. →
-  [subagent](docs/tools/subagent.md)
+  [subagent](docs/2-handbook/tools/subagent.md)
 - **forge** — its own Forgejo account, the `hive-forge` CLI, git
   credentials, and notifications turned into todos. Optional linked
   accounts on other forges, GitLab (`glab` + push), and GitHub (`gh` + push) via
   `services.hyperhive.agent.github.enable`. →
-  [forge](docs/integrations/forge.md) · [gitlab](docs/integrations/gitlab.md) ·
-  [github](docs/integrations/github.md)
+  [forge](docs/2-handbook/integrations/forge.md) · [gitlab](docs/2-handbook/integrations/gitlab.md) ·
+  [github](docs/2-handbook/integrations/github.md)
 - **matrix** — its own account(s) on the swarm homeserver, as MCP tools. →
-  [matrix](docs/tools/matrix.md)
+  [matrix](docs/2-handbook/tools/matrix.md)
 - **knowledge** — the swarm's shared `internal/knowledge` repo, read-only
   at `/knowledge`, plus hyperhive's own docs in the container. →
-  [knowledge](docs/integrations/knowledge.md)
+  [knowledge](docs/2-handbook/integrations/knowledge.md)
 - **web UI** — a per-agent page behind the gateway: live terminal of the
   turn stream, model / effort switching, cancel.
 - **GUI** (opt-in, `services.hyperhive.agent.gui.enable`) — a Wayland
@@ -106,7 +106,7 @@ box it gets:
   the web UI.
 - **reverse engineering** (opt-in, `services.hyperhive.agent.rea.enable`, or the
   `reverse-engineer` archetype) — REA and Ghidra 12.1 in the container, with
-  their MCP tools allowed. → [archetypes](docs/swarm/archetypes.md)
+  their MCP tools allowed. → [archetypes](docs/2-handbook/swarm/archetypes.md)
 - **your own tools** — any extra MCP server (stdio or http) via
   `services.hyperhive.agent.extraMcpServers`, and any NixOS config you'd
   put on a machine.
@@ -114,7 +114,7 @@ box it gets:
 ## Quick start: an all-local swarm
 
 The whole swarm on one box — a hive plus every shared service. Good for a
-dev box or a single-host deployment; [`docs/swarm/`](docs/swarm/README.md)
+dev box or a single-host deployment; [`docs/swarm/`](docs/2-handbook/swarm/README.md)
 covers spreading a swarm across hosts.
 
 ```nix
@@ -158,7 +158,7 @@ After `nixos-rebuild switch` the swarm UI answers on the swarm domain, and
 the hive brings up the manager agent (`ruth`). A few steps stay
 deliberately human — initialising the secret store, giving ruth her store
 identity, creating your SSO account. Walk through
-**[`docs/getting-started/setup.md`](docs/getting-started/setup.md)**
+**[`docs/1-getting-started/setup.md`](docs/1-getting-started/setup.md)**
 once, top to bottom.
 
 ## Operating it
@@ -167,14 +167,14 @@ once, top to bottom.
   (`admins` group): hive roster and status, every agent with its live
   terminal and wanted state, creating agents, linking external forge and
   matrix accounts, the job graph, a cross-repo issue report. →
-  [`docs/swarm/ui.md`](docs/swarm/ui.md)
+  [`docs/2-handbook/swarm/ui.md`](docs/2-handbook/swarm/ui.md)
 - **`swarmctl`** — the swarm's CLI, on the swarm-controller host: create
   agents and mint their identities, manage SSO users, make forge admins.
-  → [reference](docs/tools/swarmctl-cli.md)
+  → [reference](docs/2-handbook/reference/swarmctl-cli.md)
 - **per-hive** — each hive's dashboard (container state,
   rebuild queue) and `hivectl` for host-level administration and
-  container shells. → [`docs/web-ui/`](docs/web-ui/README.md) ·
-  [hivectl](docs/tools/hivectl.md)
+  container shells. → [`docs/web-ui/`](docs/2-handbook/web-ui/README.md) ·
+  [hivectl](docs/2-handbook/tools/hivectl.md)
 
 You are an SSO user too: `swarmctl user add <you> --group admins`, and a
 first login through authelia creates your forge and matrix accounts;
@@ -187,10 +187,10 @@ one becomes a homeserver admin within five minutes of that first login.
 pick the page for your task rather than reading front to back. Some
 common entry points:
 
-- connecting hives into a swarm → [`swarm/`](docs/swarm/README.md)
-- how config changes flow → [`agent-lifecycle/config-changes.md`](docs/agent-lifecycle/config-changes.md)
-- trust boundary + threat model → [`trust-boundary/`](docs/trust-boundary/boundary.md)
-- what an agent's turn looks like → [`turn-loop/`](docs/turn-loop/README.md)
+- connecting hives into a swarm → [`swarm/`](docs/2-handbook/swarm/README.md)
+- how config changes flow → [`agent-lifecycle/config-changes.md`](docs/2-handbook/agent-lifecycle/config-changes.md)
+- trust boundary + threat model → [`trust-boundary/`](docs/2-handbook/trust-boundary/boundary.md)
+- what an agent's turn looks like → [`turn-loop/`](docs/4-implementation/turn-loop/README.md)
 - every `services.hyperhive.*` option → [options reference](https://hyperhive.darkest.space/options/)
 
 ## Hacking on it
@@ -205,6 +205,6 @@ sudo nixos-rebuild switch --flake .#<host>
 ```
 
 Conventions (commit style, no `#[allow(clippy::…)]`, the pre-push hook)
-live in [`docs/process/conventions.md`](docs/process/conventions.md).
+live in [`docs/5-project/process/conventions.md`](docs/5-project/process/conventions.md).
 Issues + backlog are on the
 [forge](https://forge.darkest.space/hyperhive/hyperhive/issues).