I am always interested in how to organize the folder architecture in a way that, in the future, it will not get in front of the development team. Example: MVC

I am always interested in how to organize the folder architecture in a way that, in the future, it will not get in front of the development team. Example: MVC was one of the go-to choices some years ago with folders /models, /view and /controllers, where everything was put in it. But, nowadays we know that it can get messy, specially when there are too many domains. Besides that, MVC isn't appropriated for the REST world (the V is not suited for that).