Program: 16998
Project: 16998
Buggy source:
public void initialize(final IPath containerPath,final IScriptProject project) throws CoreException {
  Job job=new Job("String_Node_Str"){
    public IStatus run(    IProgressMonitor monitor){
      try {
        IFile getZipFile=project.getProject().getFile(containerPath.lastSegment());
        String groupName=getZipFile.getFullPath().lastSegment();
        IFile zipfile=project.getProject().getFile(groupName);
        BuildPathUtils.initGroupWithTypeList(groupName,zipfile);
        BuildPathUtils.addLinkForGroup(groupName,groupName);
        System.out.println(containerPath);
        System.out.println(project);
        VJETZipContainer container=new VJETZipContainer(groupName,zipfile.getFullPath());
        container.setEntries(createEntries(groupName,getZipFile.getFullPath()));
        DLTKCore.setBuildpathContainer(containerPath,new IScriptProject[]{project},new IBuildpathContainer[]{container},null);
      }
 catch (      CoreException e) {
        return e.getStatus();
      }
 finally {
        monitor.done();
      }
      return Status.OK_STATUS;
    }
    private List createEntries(    String groupName,    IPath containerPath){
      List entries=new ArrayList(1);
      IBuildpathAttribute[] attributes=new IBuildpathAttribute[0];
      ArrayList excluded=new ArrayList();
      entries.add(new BuildpathEntry(IProjectFragment.K_BINARY,IBuildpathEntry.BPE_LIBRARY,ScriptProject.canonicalizedPath(BuildPathUtils.createPathForGroup(groupName)),false,BuildpathEntry.INCLUDE_ALL,(IPath[])excluded.toArray(new IPath[excluded.size()]),EMPTY_RULES,false,attributes,false));
      entries.add(new BuildpathEntry(IProjectFragment.K_BINARY,IBuildpathEntry.BPE_LIBRARY,ScriptProject.canonicalizedPath(containerPath),false,BuildpathEntry.INCLUDE_ALL,(IPath[])excluded.toArray(new IPath[excluded.size()]),EMPTY_RULES,false,attributes,false));
      return entries;
    }
  }
;
  job.setRule(ResourcesPlugin.getWorkspace().getRoot());
  job.schedule();
}

Fixed version (ground truth):
public void initialize(final IPath containerPath,final IScriptProject project) throws CoreException {
  Job job=new Job("String_Node_Str"){
    public IStatus run(    IProgressMonitor monitor){
      try {
        IFile getZipFile=project.getProject().getFile(containerPath.lastSegment());
        String groupName=getZipFile.getFullPath().lastSegment();
        IFile zipfile=project.getProject().getFile(groupName);
        BuildPathUtils.initGroupWithTypeList(groupName,zipfile);
        BuildPathUtils.addLinkForGroup(groupName,groupName);
        VJETZipContainer container=new VJETZipContainer(groupName,zipfile.getFullPath());
        container.setEntries(createEntries(groupName,getZipFile.getFullPath()));
        DLTKCore.setBuildpathContainer(containerPath,new IScriptProject[]{project},new IBuildpathContainer[]{container},null);
      }
 catch (      CoreException e) {
        return e.getStatus();
      }
 finally {
        monitor.done();
      }
      return Status.OK_STATUS;
    }
    private List createEntries(    String groupName,    IPath containerPath){
      List entries=new ArrayList(1);
      IBuildpathAttribute[] attributes=new IBuildpathAttribute[0];
      ArrayList excluded=new ArrayList();
      entries.add(new BuildpathEntry(IProjectFragment.K_BINARY,IBuildpathEntry.BPE_LIBRARY,ScriptProject.canonicalizedPath(containerPath),false,BuildpathEntry.INCLUDE_ALL,(IPath[])excluded.toArray(new IPath[excluded.size()]),EMPTY_RULES,false,attributes,false));
      entries.add(new BuildpathEntry(IProjectFragment.K_BINARY,IBuildpathEntry.BPE_LIBRARY,ScriptProject.canonicalizedPath(BuildPathUtils.createPathForGroup(groupName)),false,BuildpathEntry.INCLUDE_ALL,(IPath[])excluded.toArray(new IPath[excluded.size()]),EMPTY_RULES,false,attributes,false));
      return entries;
    }
  }
;
  job.setRule(ResourcesPlugin.getWorkspace().getRoot());
  job.schedule();
}