Program: 44618
Project: 44618
Buggy source:
/** 
 * {@inheritDoc}
 */
@Override public void generate(Set<? extends TypeElement> annotations,RoundEnvironment roundEnv){
  Set<? extends TypeElement> typesElement=ElementFilter.typesIn(roundEnv.getRootElements());
  for (  TypeElement element : typesElement) {
    if (element.getKind().isInterface() && element.getModifiers().contains(Modifier.PUBLIC)) {
      MessageBundle bundleAnnotation=element.getAnnotation(MessageBundle.class);
      MessageLogger loggerAnnotation=element.getAnnotation(MessageLogger.class);
      if (bundleAnnotation != null || loggerAnnotation != null) {
        PackageElement packageElement=elementUtils.getPackageOf(element);
        String packageName=packageElement.getQualifiedName().toString();
        String interfaceName=element.getSimpleName().toString();
        String primaryClassName=TransformationUtil.toQualifiedClassName(packageName,interfaceName.concat(bundleAnnotation != null ? "String_Node_Str" : "String_Node_Str"));
        Class<?> annotationClass=bundleAnnotation != null ? MessageBundle.class : MessageLogger.class;
        try {
          FileObject fObj=filer.getResource(StandardLocation.CLASS_OUTPUT,packageName,interfaceName);
          String packagePath=fObj.toUri().getPath().replaceAll(interfaceName,"String_Node_Str");
          File dir=new File(packagePath);
          File[] files=dir.listFiles(new TranslationFileFilter(interfaceName));
          for (          File file : files) {
            String qualifiedClassName=primaryClassName + TranslationUtil.getTranslationClassNameSuffix(file.getName());
            this.messager.printMessage(Diagnostic.Kind.NOTE,String.format("String_Node_Str",qualifiedClassName,packageName));
            this.generateClassFor(primaryClassName,qualifiedClassName,annotationClass,file);
          }
        }
 catch (        IOException e) {
          this.messager.printMessage(Diagnostic.Kind.ERROR,String.format("String_Node_Str",packageName));
        }
      }
    }
  }
}

Fixed version (ground truth):
/** 
 * {@inheritDoc}
 */
@Override public void generate(Set<? extends TypeElement> annotations,RoundEnvironment roundEnv){
  Set<? extends TypeElement> typesElement=ElementFilter.typesIn(roundEnv.getRootElements());
  for (  TypeElement element : typesElement) {
    if (element.getKind().isInterface() && element.getModifiers().contains(Modifier.PUBLIC)) {
      MessageBundle bundleAnnotation=element.getAnnotation(MessageBundle.class);
      MessageLogger loggerAnnotation=element.getAnnotation(MessageLogger.class);
      if (bundleAnnotation != null || loggerAnnotation != null) {
        PackageElement packageElement=elementUtils.getPackageOf(element);
        String packageName=packageElement.getQualifiedName().toString();
        String interfaceName=element.getSimpleName().toString();
        String primaryClassName=TransformationUtil.toQualifiedClassName(packageName,interfaceName.concat(bundleAnnotation != null ? "String_Node_Str" : "String_Node_Str"));
        Class<?> annotationClass=bundleAnnotation != null ? MessageBundle.class : MessageLogger.class;
        try {
          FileObject fObj=filer.getResource(StandardLocation.CLASS_OUTPUT,packageName,interfaceName);
          String packagePath=fObj.toUri().getPath().replaceAll(interfaceName,"String_Node_Str");
          File dir=new File(packagePath);
          File[] files=dir.listFiles(new TranslationFileFilter(interfaceName));
          if (files != null) {
            for (            File file : files) {
              String qualifiedClassName=primaryClassName + TranslationUtil.getTranslationClassNameSuffix(file.getName());
              this.messager.printMessage(Diagnostic.Kind.NOTE,String.format("String_Node_Str",qualifiedClassName,packageName));
              this.generateClassFor(primaryClassName,qualifiedClassName,annotationClass,file);
            }
          }
        }
 catch (        IOException e) {
          this.messager.printMessage(Diagnostic.Kind.ERROR,String.format("String_Node_Str",packageName));
        }
      }
    }
  }
}