[Major] Switching Model::Index from int to std::size_t

src/algorithm/center-of-mass.hpp

src/algorithm/cholesky.hpp

src/algorithm/crba.hpp

src/algorithm/jacobian.hpp

src/algorithm/kinematics.hpp

src/algorithm/rnea.hpp

src/multibody/model.hpp

src/python/data.hpp

src/python/eigen_container.hpp

src/simulation/compute-all-terms.hpp

unittest/cholesky.cpp

unittest/jacobian.cpp

unittest/joints.cpp

unittest/symmetric.cpp