1) eliminate methods no longer return a shared pointer. Shared pointers are good for Factors and Conditionals (which are also non-copyable), because these are often passed around under the hood. However, a BayesNet is simple a list of shared pointers and hence does not cost a lot to return as an object (which is compiler-optimized anyway: there is no copy). So, the signature of all eliminate methods changed to simply return a BayesNet<> object (not a shared pointer).
2) GaussianBayesNet::optimize is now replaced by optimize(GaussianBayesNet) and returns a VectorConfig and not a shared pointer
3) GaussianBayesNet and SymbolicBayesNet are now simply typedefs, not derived classes. This is desirable because the BayesTree class uses templated methods that return BayesNet<Conditional>, not a specific BayesNet derived class.
The main renaming that happened is
BayesChain -> BayesNet
ChordalBayesNet -> GaussianBayesNet == BayesNet<ConditionalGaussian>
SymbolicBayesChain -> SymbolicBayesNet == BayesNet<SymbolicConditional>
Frank Dellaert