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

@@ -0,0 +1,20 @@
+{ config, inputs, ... }:
+# Global agent skills from the skills flake, placed under the agent harness's
+# 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;
+
+  # The skills installed globally, as derivations from the skills flake.
+  skills = [ ];
+in
+{
+  home-manager.sharedModules = [ inputs.skills.homeModules.default ];
+  home-manager.users.${user}.programs.agents.skills = skills;
+}