Refactor layouts and animations to be more modular; fix animation flicker

[emlun]

This is a quite substantial refactoring of the component structure, with the following goals:

• Abstract the fade-in animation as a simple reusable component
• Decouple <Layout> from <PrivateRoute> and other state, making it purely a layout component
  • The warning about notification issues is moved to <PrivateRoute.NotificationPermissionWarning>
• Apply the fade-in animation at the layout/route level instead of explicitly in each component

• Fix the noticeable flicker in the fade-in animation

  Animation flicker before ff06316

  [fade-in-flicker.webm](https://github.com/user-attachments/assets/f16931b5-1208-4a8a-bb4e-59a31970ae50)

  Animation flicker fixed in ff06316

  [fade-in-no-flicker.webm](https://github.com/user-attachments/assets/1921561d-2d14-4ae4-a8f8-9d0d8503a9fb)

I think these changes improve separation of concerns between these components, which helps keep them modular and easy to work with.