Peter doesn't seem to release bnd to public repos, but does have an accessible private repo. The bundle plugin can copy bnd into itself so users don't have to have peter's secret stash configured in their nexus repo manager.
Patch does this and upgrades to latest bnd. I can't see any reason to keep the copied Builder source – plugin passes tests and appears to work without it – so I removed it. You'll need to run
svn rm src/main/java/aQute/lib/osgi/Builder.java
Also the code in src/main/java/org/apache/felix/bundleplugin/PackageVersionAnalyzer.java really doesn't compile any more and I suspect the functionality has moved into bnd. However I can't actually tell what its trying to do; I commented it out. If this functionality is actually in bnd then removing the class would be a good idea.