## What happened

After updating 4.0.2 → 4.0.4, the **Apps** submenu of a cloned menu plugin (`omarchy plugin clone omarchy.menu` → `jr.menu`) shows "Nothing here yet" for every application. Searching for an app name from the root menu finds only non-app rows (e.g. Setup › Defaults › Browser). Newly installed apps (Google Chrome in my case) therefore never appear in the menu.

The stock `omarchy.menu` lists apps normally. Disabling the clone and enabling the stock plugin fixes it immediately, with the clone's `Menu.qml` otherwise byte-identical to the shipped one apart from an unrelated keybinding tweak.

## Expected

A cloned menu plugin should list applications exactly like the stock plugin, since cloning is the supported way to customise it.

## Steps to reproduce

1. `omarchy plugin clone omarchy.menu` (no edits needed), make sure the clone is the enabled menu.
2. `omarchy-restart-shell`
3. Open the menu → **Apps**. It shows "Nothing here yet".
4. `omarchy-shell shell setPluginEnabled <clone-id> false; omarchy-shell shell setPluginEnabled omarchy.menu true` → Apps is populated again.

## Root cause

Adding `console.log` to the clone shows `root.shell` is a `PluginShellApi` whose `appLibrary` is **null from the moment it is assigned** (not destroyed later).

In `shell/shell.qml`:

- `pluginShellFor(manifest)` returns the real shell for first-party plugins, but for third-party plugins calls `createScopedPluginShell(manifest, …)`, which sets
  `appLibrary: shell.manifestHasKind(manifest, "menu") ? shell.pluginAppLibraryFor(cacheKey, key) : null`.
- `manifestHasKind()` is `Array.isArray(manifest.kinds) && manifest.kinds.indexOf(kind) !== -1`.
- Panel/overlay/menu plugins are loaded by an `Instantiator` over `shell.panelEntries`, and the delegate passes `panelEntry.manifest` (i.e. `modelData.manifest`) into `pluginShellFor()`.

Going through the Instantiator's `modelData` converts the nested `kinds` array into a `QVariantList`, which QML exposes as a `V4Sequence`, **not** a JS Array. So `Array.isArray(manifest.kinds)` is `false`, `manifestHasKind()` returns `false`, and the scoped shell gets `appLibrary: null`. `indexOf` still works on the sequence, which is why `computePanelEntries()` and `isEnabled()` are unaffected and the plugin still loads — only the `Array.isArray` guard breaks.

Minimal reproduction, run with `quickshell -p`:

```qml
import QtQuick
import Quickshell
ShellRoot {
  id: shell
  property var entries: [{ id: "x", manifest: { kinds: ["menu", "bar-widget"] } }]
  function hasKind(m, k) { return !!m && Array.isArray(m.kinds) && m.kinds.indexOf(k) !== -1 }
  Instantiator {
    model: shell.entries
    delegate: QtObject {
      required property var modelData
      Component.onCompleted: console.log(
        "direct=" + Array.isArray(shell.entries[0].manifest.kinds)
        + " viaModelData=" + Array.isArray(modelData.manifest.kinds)
        + " hasKind=" + shell.hasKind(modelData.manifest, "menu")
        + " type=" + Object.prototype.toString.call(modelData.manifest.kinds))
    }
  }
}
```

Output on this system:

```
direct=true viaModelData=false hasKind=false type=[object V4Sequence]
```

First-party plugins never hit this because `pluginShellFor()` short-circuits to the host shell before the kind check.

## Suggested fix

Either look the manifest up fresh in the Instantiator delegate instead of using `modelData`:

```qml
if ("shell" in item) item.shell = shell.pluginShellFor(shell.pluginRegistry.installedPlugins[panelEntry.pluginId])
```

or make `manifestHasKind()` tolerant of sequences:

```qml
function manifestHasKind(manifest, kind) {
  var kinds = manifest && manifest.kinds
  return !!kinds && typeof kinds.indexOf === "function" && kinds.indexOf(kind) !== -1
}
```

(`createScopedPluginShell` and `pluginShellCapabilityProfile` call `manifestHasKind` with the same object, so the profile cache key is consistent either way.)

## Environment

- `omarchy version`: 4.0.4-1 (also present in current `master` `shell/shell.qml`, `manifestHasKind` at ~line 354 and the `panelEntry.manifest` hand-off at ~line 1384)
- quickshell 0.3.1-1, qt6-declarative 6.11.2-1, hyprland 0.56.2-2
- Kernel 7.2.5-3-omarchy, Dell Latitude 7450, x86_64

Workaround until fixed: in the clone's `Menu.qml`, `import qs.services`, declare `property AppLibrary localAppLibrary: AppLibrary { }` and make `appLibrary` fall back to it when `root.shell.appLibrary` is null.

Filed by Claude Fable 5.1 via Claude Code.