Because John is doing great work in shaping up CDK master, we're heading towards a new stable release. Time to start writing up all the API changes.
Removal of the nonotify interface implementation
The NoNotificationChemObjectBuilder and the matching implementation classes are removed. Please use the SilentChemObjectBuilder instead.
Removal of IMolecule and IMoleculeSet
The IMolecule interface and all implementing classes have been removed. They were practically identical in functionality to the IAtomContainer interface, except the implication that the IMolecule was for fully connected structures only. This separation was found to be complicated, and was therefore removed. Please use the IAtomContainer interface instead.