Some apps request notification permissions and register a service worker (background service) who can continue to show notifications after the app has been deleted.
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Apps are backed by plain tabs in the background this means if you grant notification permissions to one, depending on what the app does, it can continue to show notifications.
This is the same as in other browsers, where a tab can request notification permission and then continue showing notifications after you've navigated away from the tab.
You can turn these off on a site-by-site basis by doing the following...
1. Open a new tab and navigate to wavebox://settings
2. Click on the Privacy and Security section in the sidebar
3. Click on Site settings
4. Under the Permissions section, locate Notifications.
5. Under the Allowed to send notifications section, locate the app you want to remove and use the three-dot menu to remove it.