Program: 109445
Project: 109445
Buggy source:
@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);
    }
  }
}

Fixed version (ground truth):
@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);
    }
  }
}