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/claude-code/skills/setup-skills/hash-dir.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+# Deterministic recursive hash of a directory's file contents.
+#
+# Hashes relative paths, not absolute ones, so two directories with
+# identical contents hash identically regardless of where they live on
+# disk (needed to compare a project's copied skill against the library
+# source it was copied from).
+#
+# Usage: hash-dir.sh <directory>
+set -euo pipefail
+
+if [ $# -ne 1 ]; then
+  echo "Usage: hash-dir.sh <directory>" >&2
+  exit 1
+fi
+
+dir="$1"
+if [ ! -d "$dir" ]; then
+  echo "Not a directory: $dir" >&2
+  exit 1
+fi
+
+(cd "$dir" && find . -type f -print0 | sort -z | xargs -0 -r sha256sum) | sha256sum | awk '{print $1}'