Bring docs/ up to date and cover the undocumented subsystems

Every reference doc was audited claim-by-claim against the code.
file-layout and omarchy-shell were the most decayed (renamed commands,
the etc/ overrides source split, dead IPC entry points and example keys);
update-process lagged the recent pipeline changes and gains a channels
section; theming and audio-tuning were accurate but thin around their
lifecycles.

New reference docs for the subsystems that had none: the menu system,
the CLI router, the notification daemon, and the non-acceptance test
architecture. AGENTS.md links the two of those agents will need most.

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

AGENTS.md

@@ -90,7 +90,8 @@ Exceptions are allowed for migration and package-helper scripts where the helper
 
 # Menu
 
-- The menu definition lives in `default/omarchy/omarchy-menu.jsonc`.
+- The menu definition lives in `default/omarchy/omarchy-menu.jsonc`;
+  [`docs/menu.md`](docs/menu.md) covers the schema, guards, and providers.
 - Do not add `aliases` to new menu entries. Aliases are reserved for
   established alternate names users already type, kept for compatibility.
 
@@ -102,7 +103,9 @@ Exceptions are allowed for migration and package-helper scripts where the helper
 
 # Tests
 
-Run focused automated tests for the area you changed. Current test entry points:
+Run focused automated tests for the area you changed;
+[`docs/testing.md`](docs/testing.md) covers how the suites are shaped. Current
+test entry points:
 
 - `./test/all` - aggregate runner for CLI and shell tests; it intentionally does not run graphical acceptance tests
 - `./test/cli` - CLI routing, command metadata, theme helpers, and safe dispatch coverage