refactor: nix/host-modules + nix/agent-modules layout, update doc paths

nix/agent-modules/packages.nix

@@ -0,0 +1,22 @@
+# The hyperhive-built packages the harness modules consume, threaded
+# in explicitly as an option — no overlay. The flake's
+# `nixosModules.{agent-base,ruth}` set this to the flake's own package
+# outputs via `lib.mkDefault`, so a per-agent override of an
+# individual key still wins.
+{ lib, ... }:
+{
+  options.hyperhive.packages = lib.mkOption {
+    type = lib.types.attrsOf lib.types.package;
+    internal = true;
+    description = ''
+      hyperhive package outputs consumed by the harness modules: the
+      per-binary daemon/CLI packages (`hive-agent`, `hive-agent-mcp`,
+      `hive-agent-wake`, `hive-bash-daemon`, `hive-bash-mcp`,
+      `hive-forge`, `hive-matrix-daemon`, `hive-matrix-mcp`,
+      `hive-metric`) plus the `assets`, `frontend` and
+      `reference-docs` trees. Wired by the flake's agent-base/ruth
+      nixosModules to `hyperhive.packages.<system>.*`; override an
+      individual key per-agent to swap in a patched binary.
+    '';
+  };
+}