Replace deprecated patterns with current API conventions:
- core.WithName/WithService → core.New() + RegisterService + RegisterAction
- mcp.WithWorkspaceRoot/WithWSHub/WithSubsystem → mcp.New(mcp.Options{})
- core.ServiceFor[T] → direct service reference
- Add cancellable context and ServiceShutdown to GUI mode
- Handle previously-discarded errors from api.New and config.New
Co-Authored-By: Virgil <virgil@lethean.io>