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/to-spec/SPEC-FORMAT.md

@@ -0,0 +1,55 @@
+# Spec Format
+
+## Template
+
+```md
+## Problem Statement
+
+The problem that the user is facing, from the user's perspective.
+
+## Solution
+
+The solution to the problem, from the user's perspective.
+
+## User Stories
+
+An extensive, numbered list of user stories, covering all aspects of the feature. Each user story should be in the format of:
+
+1. As an <actor>, I want a <feature>, so that <benefit>
+
+<user-story-example>
+1. As a mobile bank customer, I want to see balance on my accounts, so that I can make better informed decisions about my spending
+</user-story-example>
+
+## Implementation Decisions
+
+A list of implementation decisions that were made. This can include:
+
+- The modules that will be built/modified
+- The interfaces of those modules that will be modified
+- Technical clarifications from the developer
+- Architectural decisions
+- Schema changes
+- API contracts
+- Specific interactions
+
+## Testing Decisions
+
+A list of testing decisions that were made. Include:
+
+- A description of what makes a good test (only test external behavior, not implementation details)
+- Which modules will be tested
+- Prior art for the tests (i.e. similar types of tests in the codebase)
+
+## Out of Scope
+
+A description of the things that are out of scope for this spec.
+
+## Further Notes
+
+Any further notes about the feature.
+```
+
+## Rules
+
+- **Don't include specific file paths or code snippets.** They may end up being outdated very quickly. Exception: if a prototype produced a snippet that encodes a decision more precisely than prose can (state machine, reducer, schema, type shape), inline it within the relevant decision in Implementation Decisions and note briefly that it came from a prototype. Trim to the decision-rich parts — not a working demo, just the important bits.