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/test-driven-development/refactoring.md

@@ -0,0 +1,10 @@
+# Refactor Candidates
+
+After TDD cycle, look for:
+
+- **Duplication** → Extract function/class
+- **Long methods** → Break into private helpers (keep tests on public interface)
+- **Shallow modules** → Combine or deepen — see DEEPENING.md in `/codebase-design` for dependency categories and seam discipline
+- **Feature envy** → Move logic to where data lives
+- **Primitive obsession** → Introduce value objects
+- **Existing code** the new code reveals as problematic