Hi Chen,
No and yes - the same functionality has been moved into the Manifold classes, which are much more general than the old Boundary classes. For example, GridGenerator::hyper_ball automatically attaches a SphericalManifold to the boundary of the input Triangulation,
which achieves the same result as attaching a HyperBallBoundary.
More information is available at the module page:
Do you need to do anything more complex than generate a spherical geometry? If not, using SphericalManifold in place of HyperBallBoundary should do most of what you need to do (though, again, this is now done automatically by the grid generator functions).
Best,
David Wells