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>

AGENTS.md

@@ -9,7 +9,15 @@ matching guide before starting:
 - [`agents/skills/icon-font.md`](agents/skills/icon-font.md) - adding branded glyphs to `default/fonts/omarchy/omarchy.ttf`
 - [`agents/skills/acceptance-tests.md`](agents/skills/acceptance-tests.md) - writing or running graphical acceptance tests under `test/acceptance.d/`
 - [`agents/skills/visual-verification.md`](agents/skills/visual-verification.md) - verifying any change with a visual effect in the running UI
-- [`docs/migrations.md`](docs/migrations.md) - creating or changing migrations under `migrations/`
+- [`agents/skills/migrations.md`](agents/skills/migrations.md) - creating or changing migrations under `migrations/`
+
+# Documentation Layout
+
+Three documentation trees, split by genre and audience:
+
+- `agents/skills/` - task procedure ("do this when doing X"), for anyone working on the codebase
+- `docs/` - reference on how the system is shaped (file layout, update pipeline, theming, shell architecture), for anyone working on the codebase; skills link here for depth
+- `manual/` - end-user documentation for using Omarchy, published; never codebase internals
 
 # Style