The classpath container support was completely rewritten for bndtools 3.0 to much more closely map to the offline compile classpath. The best mapping we could figure out for eclipse can result in both the source folder (src) and the jar (generated/.jar) being on the eclipse classpath. We could have just put the jar (which is the best representation of the offline compile classpath), but wanted to also put the src there so F3 would take you to editable source code.
This does result in two versions of the source when searching which can be a bit annoying. If someone is an Eclipse classpath container guru and can suggest improvements, I would really love to see them!