Fixes https://github.com/flutter/flutter/issues/68253

Remove Linux shell window_configuration.cc/.h

It was a temporary solution while the shell was changing.

The previous call set the minimum size, not just the initial size.

Updates the tooling to use the GTK embedding, rather than the GLFW embedding:
- Adds new requirements to `doctor`
- Updates the app and plugin templates to make GTK-based runners and plugins
- Stops downloading and installing the GLFW artifacts

Final part of #54860, other than cleanup.