(I reported this issue in github because I hadn't read Buildr's contribution policy. See https://github.com/apache/buildr/pull/3)
See https://gist.github.com/1605072 in order to reproduce the bug. In summary, if you use Drools, it already ships a JRE container. Since the user's dependencies are written first to '.classpath' , Drools container will be taken instead of Eclipse's. In my case, it produces undesired effects like disabling Java Generics because I use the last JDK in Eclipse whereas Drools doesn't.
It makes sense to me to have JRE libs before user libs but I ignore if this change might have side effects. This bug might potentially affect any dependency making use of its own embedded JRE (i.e.: rather unlikely).