Program: 65944
Project: 65944
Buggy source:
private List<String> resolveClasspathEntries(IClasspathEntry[] classpathEntries,boolean needExported,IJavaProject project){
  ArrayList<String> newClassPath=new ArrayList<String>();
  IWorkspace space=ResourcesPlugin.getWorkspace();
  IWorkspaceRoot root=space.getRoot();
  for (int i=0; i < classpathEntries.length; i++) {
    IClasspathEntry curr=classpathEntries[i];
    if (!needExported && !curr.isExported()) {
      continue;
    }
    IPath path=curr.getPath();
    if (curr.getEntryKind() == IClasspathEntry.CPE_VARIABLE) {
      path=JavaCore.getClasspathVariable(path.segment(0));
    }
 else {
      path=JavaCore.getResolvedClasspathEntry(curr).getPath();
    }
    if (project != null && curr.getEntryKind() == IClasspathEntry.CPE_CONTAINER) {
      try {
        IClasspathContainer contianer=JavaCore.getClasspathContainer(path,project);
        if (contianer != null && contianer.getKind() == IClasspathContainer.K_APPLICATION) {
          IClasspathEntry[] entrys=contianer.getClasspathEntries();
          List<String> list=resolveClasspathEntries(entrys,needExported,project);
          for (int j=0; j < list.size(); j++) {
            addToList(newClassPath,list.get(j));
          }
        }
      }
 catch (      JavaModelException e) {
      }
      continue;
    }
    if (curr.getEntryKind() == IClasspathEntry.CPE_SOURCE) {
      path=curr.getOutputLocation();
    }
    if (path == null) {
      continue;
    }
    if (curr.getEntryKind() == IClasspathEntry.CPE_PROJECT) {
      if (root.findMember(path) instanceof IProject) {
        List<String> strs=getProjectClasspath((IProject)root.findMember(path),false,false);
        for (int j=0; j < strs.size(); j++) {
          addToList(newClassPath,strs.get(j));
        }
      }
    }
 else     if (curr.getEntryKind() == IClasspathEntry.CPE_LIBRARY || curr.getEntryKind() == IClasspathEntry.CPE_VARIABLE || curr.getEntryKind() == IClasspathEntry.CPE_SOURCE) {
      boolean inWorkSpace=true;
      if (space == null || space.getRoot() == null) {
        inWorkSpace=false;
      }
      if (root.findMember(path) == null) {
        inWorkSpace=false;
      }
      if (inWorkSpace) {
        String absPath=getFullPath(path,root.findMember(path).getProject());
        newClassPath.add(absPath);
      }
 else {
        newClassPath.add(curr.getPath().toFile().getAbsolutePath());
      }
    }
  }
  return newClassPath;
}

Fixed version (ground truth):
private List<String> resolveClasspathEntries(IClasspathEntry[] classpathEntries,boolean needExported,IJavaProject project){
  ArrayList<String> newClassPath=new ArrayList<String>();
  IWorkspace space=ResourcesPlugin.getWorkspace();
  IWorkspaceRoot root=space.getRoot();
  for (int i=0; i < classpathEntries.length; i++) {
    IClasspathEntry curr=classpathEntries[i];
    if (!needExported && !curr.isExported() && curr.getEntryKind() != IClasspathEntry.CPE_VARIABLE) {
      continue;
    }
    IPath path=curr.getPath();
    if (curr.getEntryKind() == IClasspathEntry.CPE_VARIABLE) {
      path=JavaCore.getClasspathVariable(path.segment(0));
    }
 else {
      path=JavaCore.getResolvedClasspathEntry(curr).getPath();
    }
    if (project != null && curr.getEntryKind() == IClasspathEntry.CPE_CONTAINER) {
      try {
        IClasspathContainer contianer=JavaCore.getClasspathContainer(path,project);
        if (contianer != null && contianer.getKind() == IClasspathContainer.K_APPLICATION) {
          IClasspathEntry[] entrys=contianer.getClasspathEntries();
          List<String> list=resolveClasspathEntries(entrys,needExported,project);
          for (int j=0; j < list.size(); j++) {
            addToList(newClassPath,list.get(j));
          }
        }
      }
 catch (      JavaModelException e) {
      }
      continue;
    }
    if (curr.getEntryKind() == IClasspathEntry.CPE_SOURCE) {
      path=curr.getOutputLocation();
    }
    if (path == null) {
      continue;
    }
    if (curr.getEntryKind() == IClasspathEntry.CPE_PROJECT) {
      if (root.findMember(path) instanceof IProject) {
        List<String> strs=getProjectClasspath((IProject)root.findMember(path),false,false);
        for (int j=0; j < strs.size(); j++) {
          addToList(newClassPath,strs.get(j));
        }
      }
    }
 else     if (curr.getEntryKind() == IClasspathEntry.CPE_LIBRARY || curr.getEntryKind() == IClasspathEntry.CPE_VARIABLE || curr.getEntryKind() == IClasspathEntry.CPE_SOURCE) {
      boolean inWorkSpace=true;
      if (space == null || space.getRoot() == null) {
        inWorkSpace=false;
      }
      if (root.findMember(path) == null) {
        inWorkSpace=false;
      }
      if (inWorkSpace) {
        String absPath=getFullPath(path,root.findMember(path).getProject());
        newClassPath.add(absPath);
      }
 else {
        newClassPath.add(path.toFile().getAbsolutePath());
      }
    }
  }
  return newClassPath;
}