### System details

AMD Ryzen AI 5 340 w/ Radeon 840M (Framework), Omarchy 4.0.4-1, Quickshell 0.3.1-1, Hyprland 0.56.2, kernel 7.2.5-3-omarchy, Wayland.

### What's wrong?

After cloning the menu plugin with the documented flow (`omarchy plugin clone omarchy.menu`), **installed applications disappear from the launcher**: searching for any installed app (e.g. `pinta` with `com.github.PintaProject.Pinta.desktop` present) returns no app rows, and the `Apps` submenu shows only "Nothing here yet". JSONC menu items and install-catalog rows still show, so the menu looks healthy - there is just never an app. No warning or error is logged.

The first-party `omarchy.menu` keeps working; only the clone is affected.

### Steps to reproduce

1. `omarchy plugin clone omarchy.menu` (creates `<user>.menu`, disables `omarchy.menu`)
2. Restart the shell (`omarchy restart shell`) or reboot
3. Open the menu (Super+Space) and type the name of any installed application
4. No app rows appear; `omarchy menu summon apps` shows an empty submenu

### Root cause (traced in shell.qml, 4.0.4)

- The panel loader injects the shell API only once, in `Loader.onLoaded`: `item.shell = shell.pluginShellFor(panelEntry.manifest)` (shell.qml:1342).
- For non-first-party plugins `pluginShellFor` returns a scoped API created by `createScopedPluginShell` and cached under the plugin id (shell.qml:739-744).
- During startup, the reconcile pass (shell.qml:797-810) calls `revokePluginShellApi` when `active` is false. `active` requires `pluginRegistry.isEnabled(pluginId)`, and for non-first-party plugins `isEnabled` resolves through the bar layout in `shell.json` - which loads asynchronously. So there is a startup window where an enabled clone looks disabled and its API is revoked.
- `revokePluginShellApi` destroys the cached QObject (`cacheWithoutKey(..., destroyValue=true)`, shell.qml:533-543, 559-567). A destroyed object assigned to the item's `shell` property becomes `null`.
- Because the menu manifest sets `keepLoaded: true`, the loader item survives and `onLoaded` never fires again - the shell API is never re-injected.
- In the cloned `Menu.qml`, `root.shell` is now `null`, so `root.appLibrary` is `null` and `mergeAppRows()` returns early (`if (!root.appLibrary) return`). Hence: zero app rows, zero log output.

Evidence from temporary instrumentation in the cloned `Menu.qml`:

```
Component.onCompleted: shell = null                          (expected)
Qt.callLater:         shell = PluginShellApi_QMLTYPE_57(...) (injection works)
Timer 500ms tick 1:   shell = null                           (already revoked, stays null)
mergeAppRows:         appLibrary = null                      (apps silently skipped)
```

### Workaround I applied locally

In the clone, fall back to Quickshell's global `DesktopEntries` when `appLibrary` is `null`: build app rows directly from `DesktopEntries.applications.values` (same `noDisplay` filtering), launch via `uwsm-app -- gtk-launch <id>.desktop` (same command `AppLibrary.launch` uses), resolve icons through the themed lookup, and re-merge on every menu open. Apps come back in search and the Apps submenu.

### Possible fix directions

- Defer startup reconcile revocation until the shell config has actually loaded (the "not enabled" signal is transient while `shell.json` is still async-loading), or
- Re-inject the (re-created) scoped API into registered panel loaders when a revoked API is replaced, or
- Have `pluginShellFor`/reconcile hand panel items a stable proxy that survives underlying API swaps.

Happy to prepare a PR for whichever direction you prefer.

### Diagnostics

`omarchy-debug` requires an interactive sudo password in this session, so the full log could not be generated; the partial log from the same machine is at `/tmp/omarchy-debug.log` (fastfetch summary: Omarchy 4.0.4, Quickshell 0.3.1, Hyprland 0.56.2, kernel 7.2.5-3-omarchy). All file/line references above are from `/usr/share/omarchy/shell/shell.qml` as shipped in 4.0.4-1.