Sort documentation by genre and document the layout

Task procedure lives in agents/skills/ (migrations.md moves there),
system-shape reference in docs/ (AUDIO-TUNING.md renamed to match),
end-user documentation in manual/. AGENTS.md now states the split.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

docs/update-process.md

@@ -30,7 +30,7 @@ The design goal is:
 
 ## Migration layout
 
-See [`migrations.md`](migrations.md) for the full migration model, authoring
+See [`migrations.md`](../agents/skills/migrations.md) for the full migration model, authoring
 guidelines, and troubleshooting notes.
 
 Migrations live in: