Program: 155817
Project: 155817
Buggy source:
/** 
 * Build the meta data structures for this class. Any errors or messages will be posted on the provided Messager.
 * @return True if meta data was correctly created and processing can continue, false otherwise.
 */
public boolean generate(ProcessingEnvironment processingEnv){
  for (  Element classElement : env.getElementsAnnotatedWith(RealmModule.class)) {
    String classSimpleName=classElement.getSimpleName().toString();
    if (!classElement.getKind().equals(ElementKind.CLASS)) {
      Utils.error("String_Node_Str",classElement);
      return false;
    }
    RealmModule module=classElement.getAnnotation(RealmModule.class);
    Utils.note("String_Node_Str" + classSimpleName);
    if (module.allClasses() && module.classes().length > 0) {
      Utils.error("String_Node_Str" + classSimpleName);
      return false;
    }
    String qualifiedName=((TypeElement)classElement).getQualifiedName().toString();
    Set<ClassMetaData> classes;
    if (module.allClasses()) {
      classes=availableClasses;
    }
 else {
      classes=new HashSet<ClassMetaData>();
      for (      Class<?> clazz : module.classes()) {
        if (!clazz.getSuperclass().toString().endsWith("String_Node_Str")) {
          Utils.error(clazz.getSimpleName() + "String_Node_Str" + "String_Node_Str");
          return false;
        }
        ClassMetaData metadata=classMetaData.get(clazz.getName());
        if (metadata == null) {
          Utils.error(Utils.stripPackage(qualifiedName) + "String_Node_Str" + "String_Node_Str");
          return false;
        }
        classes.add(metadata);
      }
    }
    if (module.library()) {
      libraryModules.put(qualifiedName,classes);
    }
 else {
      modules.put(qualifiedName,classes);
    }
  }
  if (modules.size() > 0 && libraryModules.size() > 0) {
    Utils.error("String_Node_Str");
    return false;
  }
  if (libraryModules.size() == 0) {
    shouldCreateDefaultModule=true;
    String defautModuleName=Constants.REALM_PACKAGE_NAME + "String_Node_Str" + Constants.DEFAULT_MODULE_CLASS_NAME;
    modules.put(defautModuleName,availableClasses);
  }
  return true;
}

Fixed version (ground truth):
/** 
 * Build the meta data structures for this class. Any errors or messages will be posted on the provided Messager.
 * @return True if meta data was correctly created and processing can continue, false otherwise.
 */
public boolean generate(ProcessingEnvironment processingEnv){
  for (  Element classElement : env.getElementsAnnotatedWith(RealmModule.class)) {
    String classSimpleName=classElement.getSimpleName().toString();
    if (!classElement.getKind().equals(ElementKind.CLASS)) {
      Utils.error("String_Node_Str",classElement);
      return false;
    }
    RealmModule module=classElement.getAnnotation(RealmModule.class);
    Utils.note("String_Node_Str" + classSimpleName);
    if (module.allClasses() && module.classes().length > 0) {
      Utils.error("String_Node_Str" + classSimpleName);
      return false;
    }
    String qualifiedName=((TypeElement)classElement).getQualifiedName().toString();
    Set<ClassMetaData> classes;
    if (module.allClasses()) {
      classes=availableClasses;
    }
 else {
      classes=new HashSet<ClassMetaData>();
      AnnotationMirror annotationMirror=null;
      for (      AnnotationMirror am : classElement.getAnnotationMirrors()) {
        if (am.getAnnotationType().toString().equals(RealmModule.class.getCanonicalName())) {
          annotationMirror=am;
          break;
        }
      }
      AnnotationValue annotationValue=null;
      for (      Map.Entry<? extends ExecutableElement,? extends AnnotationValue> entry : annotationMirror.getElementValues().entrySet()) {
        if (entry.getKey().getSimpleName().toString().equals("String_Node_Str")) {
          annotationValue=entry.getValue();
          break;
        }
      }
      List<? extends AnnotationValue> moduleClasses=(List<? extends AnnotationValue>)annotationValue.getValue();
      for (      AnnotationValue classMirror : moduleClasses) {
        String fullyQualifiedClassName=classMirror.getValue().toString();
        ClassMetaData metadata=classMetaData.get(fullyQualifiedClassName);
        if (metadata == null) {
          Utils.error(Utils.stripPackage(fullyQualifiedClassName) + "String_Node_Str" + "String_Node_Str");
          return false;
        }
        classes.add(metadata);
      }
    }
    if (module.library()) {
      libraryModules.put(qualifiedName,classes);
    }
 else {
      modules.put(qualifiedName,classes);
    }
  }
  if (modules.size() > 0 && libraryModules.size() > 0) {
    Utils.error("String_Node_Str");
    return false;
  }
  if (libraryModules.size() == 0) {
    shouldCreateDefaultModule=true;
    String defautModuleName=Constants.REALM_PACKAGE_NAME + "String_Node_Str" + Constants.DEFAULT_MODULE_CLASS_NAME;
    modules.put(defautModuleName,availableClasses);
  }
  return true;
}