There are a number of classes in IMP.core which have been marked as
deprecated for a while. I would be good to get rid of them entirely
before the first public release. I propose that after the first marked
stable version (a concept which will be explained in a forthcoming
email from Ben), I remove them from SVN.
So please check your code to make sure you don't use them and if you
do, start migrating to the replacement classes. You can find a list of
such classes at <https://salilab.org/imp/doc/doxygen/deprecated.html>
and you code should spit out warning messages whenever you create an
instance of such a class.