refactor: mirror module namespaces to their directories (task 0031)

Adopt the convention that a Module's option path mirrors its directory
under modules/, with an index file naming the directory's own segment.

- Group agent Modules under modules.agents.*: claude-code (whole
  directory), pi (flattened to a file), skills (renamed from
  agent-skills), and gitea-axi under an agents/tools/ subgroup. The
  agents/ and tools/ folders are pure namespace prefixes with no
  aggregator enable.
- Nest hypridle and hyprlock under modules.desktop.hyprland.*, with
  hyprland.nix as the index, and update the desktop aggregator.
- Remove the obsolete example Module.
- Record the convention in CONTEXT.md and ADR 0004, and update the
  neogaia host, the two live CLAUDE.md gotchas, and the skills Module's
  intentional Enable-convention exception comment.

modules/agents/skills.nix

@@ -3,6 +3,11 @@
 # skills directory so they are active in every project. The flake's home-manager
 # module self-gates on the harness being enabled and installs nothing for an
 # empty selection, so a host without one carries no skills either way.
+#
+# Unlike every other module, this one declares no `enable` flag and wires
+# unconditionally, by design.
+# The flake's self-gating above already makes it inert where the harness is
+# absent, so a gate would guard nothing.
 let
   user = config.user.name;
 

modules/example.nix

@@ -1,13 +0,0 @@
-{ config, lib, ... }:
-# Reference example for the module shape: imported unconditionally, but inert
-# until a host sets its `enable` flag.
-let
-  cfg = config.modules.example;
-in
-{
-  options.modules.example.enable = lib.mkEnableOption "the reference example module";
-
-  config = lib.mkIf cfg.enable {
-    environment.etc."skeleton-example".text = "This Module is enabled.\n";
-  };
-}