Program: 109444
Project: 109444
Buggy source:
@Override public Configuration getConfiguration(GraphContext context){
  GraphOperation copyConfigToGraph=new GraphOperation(){
    @Override public void perform(    GraphRewrite event,    EvaluationContext context){
      Map<String,Object> config=event.getGraphContext().getOptionMap();
      Boolean sourceMode=(Boolean)config.get(SourceModeOption.NAME);
      @SuppressWarnings("String_Node_Str") List<String> includeJavaPackages=(List<String>)config.get(ScanPackagesOption.NAME);
      @SuppressWarnings("String_Node_Str") final List<String> excludeJavaPackages;
      if (config.get(ExcludePackagesOption.NAME) == null)       excludeJavaPackages=new ArrayList<>();
 else       excludeJavaPackages=new ArrayList<>((List<String>)config.get(ExcludePackagesOption.NAME));
      Predicate<File> predicate=new FileSuffixPredicate("String_Node_Str");
      Visitor<File> visitor=new Visitor<File>(){
        @Override public void visit(        File file){
          try (FileInputStream inputStream=new FileInputStream(file)){
            LineIterator it=IOUtils.lineIterator(inputStream,"String_Node_Str");
            while (it.hasNext()) {
              String line=it.next();
              if (!line.startsWith("String_Node_Str") && !line.trim().isEmpty()) {
                excludeJavaPackages.add(line);
              }
            }
          }
 catch (          Exception e) {
            throw new WindupException("String_Node_Str" + file.toString() + "String_Node_Str",e);
          }
        }
      }
;
      FileVisit.visit(PathUtil.getUserIgnoreDir().toFile(),predicate,visitor);
      FileVisit.visit(PathUtil.getWindupIgnoreDir().toFile(),predicate,visitor);
      WindupJavaConfigurationModel javaConfiguration=WindupJavaConfigurationService.getJavaConfigurationModel(event.getGraphContext());
      javaConfiguration.setSourceMode(sourceMode == null ? false : sourceMode);
      javaConfiguration.setScanJavaPackageList(includeJavaPackages);
      javaConfiguration.setExcludeJavaPackageList(excludeJavaPackages);
      List<File> additionalClasspaths=(List<File>)config.get(AdditionalClasspathOption.NAME);
      if (additionalClasspaths != null) {
        FileService fileService=new FileService(event.getGraphContext());
        for (        File file : additionalClasspaths) {
          FileModel fileModel=fileService.createByFilePath(file.getAbsolutePath());
          javaConfiguration.addAdditionalClasspath(fileModel);
        }
      }
    }
  }
;
  return ConfigurationBuilder.begin().addRule().perform(copyConfigToGraph);
}

Fixed version (ground truth):
@Override public Configuration getConfiguration(GraphContext context){
  GraphOperation copyConfigToGraph=new GraphOperation(){
    @Override public void perform(    GraphRewrite event,    EvaluationContext context){
      Map<String,Object> config=event.getGraphContext().getOptionMap();
      Boolean sourceMode=(Boolean)config.get(SourceModeOption.NAME);
      Boolean enableClassFoundFoundAnalysis=(Boolean)config.get(EnableClassNotFoundAnalysisOption.NAME);
      @SuppressWarnings("String_Node_Str") List<String> includeJavaPackages=(List<String>)config.get(ScanPackagesOption.NAME);
      @SuppressWarnings("String_Node_Str") final List<String> excludeJavaPackages;
      if (config.get(ExcludePackagesOption.NAME) == null)       excludeJavaPackages=new ArrayList<>();
 else       excludeJavaPackages=new ArrayList<>((List<String>)config.get(ExcludePackagesOption.NAME));
      Predicate<File> predicate=new FileSuffixPredicate("String_Node_Str");
      Visitor<File> visitor=new Visitor<File>(){
        @Override public void visit(        File file){
          try (FileInputStream inputStream=new FileInputStream(file)){
            LineIterator it=IOUtils.lineIterator(inputStream,"String_Node_Str");
            while (it.hasNext()) {
              String line=it.next();
              if (!line.startsWith("String_Node_Str") && !line.trim().isEmpty()) {
                excludeJavaPackages.add(line);
              }
            }
          }
 catch (          Exception e) {
            throw new WindupException("String_Node_Str" + file.toString() + "String_Node_Str",e);
          }
        }
      }
;
      FileVisit.visit(PathUtil.getUserIgnoreDir().toFile(),predicate,visitor);
      FileVisit.visit(PathUtil.getWindupIgnoreDir().toFile(),predicate,visitor);
      WindupJavaConfigurationModel javaConfiguration=WindupJavaConfigurationService.getJavaConfigurationModel(event.getGraphContext());
      javaConfiguration.setSourceMode(sourceMode == null ? false : sourceMode);
      javaConfiguration.setScanJavaPackageList(includeJavaPackages);
      javaConfiguration.setExcludeJavaPackageList(excludeJavaPackages);
      javaConfiguration.setClassNotFoundAnalysisEnabled(enableClassFoundFoundAnalysis == null ? false : enableClassFoundFoundAnalysis);
      List<File> additionalClasspaths=(List<File>)config.get(AdditionalClasspathOption.NAME);
      if (additionalClasspaths != null) {
        FileService fileService=new FileService(event.getGraphContext());
        for (        File file : additionalClasspaths) {
          FileModel fileModel=fileService.createByFilePath(file.getAbsolutePath());
          javaConfiguration.addAdditionalClasspath(fileModel);
        }
      }
    }
  }
;
  return ConfigurationBuilder.begin().addRule().perform(copyConfigToGraph);
}