app: remove legacy manifest update-flag handling in create-reducer.ts

In `packages/modules/app/src/app/create-reducer.ts`, the `setManifest` reducer case branches on `action.meta.update` to merge vs. replace the manifest, with a note that this is legacy behavior:

```ts
// TODO: after legacy is removed, remove the update flag
if (action.meta.update) {
state.manifest = Object.assign(state.manifest ?? {}, action.payload);
} else {
state.manifest = action.payload;
}
```

Remove the `update` flag branch once the legacy manifest-merge behavior is no longer needed.

Start in packages/modules/app/src/app/create-reducer.ts at the setManifest reducer case, then search the app module for references to action.meta.update and the legacy merge behavior. Done means the obsolete update-flag branch and its remaining references are removed without changing the replacement behavior.

Written by the indexing model from the issue text.