Program: 11064
Project: 11064
Buggy source:
public static void main(String[] args) throws IOException, InterruptedException {
  OptionParser parser=new OptionParser();
  OptionSpec<File> input=parser.accepts("String_Node_Str").withRequiredArg().ofType(File.class).required();
  OptionSpec<File> model=parser.accepts("String_Node_Str").withRequiredArg().ofType(File.class);
  OptionSpec<File> output=parser.accepts("String_Node_Str").withRequiredArg().ofType(File.class);
  OptionSpec<Format> format=parser.accepts("String_Node_Str").withRequiredArg().ofType(Format.class).defaultsTo(Format.XML);
  OptionSpec verify=parser.accepts("String_Node_Str");
  OptionSpec optimization=parser.accepts("String_Node_Str");
  OptionSpec annotations=parser.accepts("String_Node_Str");
  OptionSet options=parser.parse(args);
  final Path source=input.value(options).toPath();
  final Path destination=output.value(options) != null ? output.value(options).toPath() : source.toFile().isDirectory() ? source : source.getParent();
  final Format outputFormat=format.value(options);
  Map<Path,Path> inOutMap=new HashMap<>();
  if (source.toFile().isDirectory()) {
    if (destination.toFile().exists() && !destination.toFile().isDirectory()) {
      throw new IllegalArgumentException("String_Node_Str");
    }
    Files.walkFileTree(source,new SimpleFileVisitor<Path>(){
      @Override public FileVisitResult visitFile(      Path file,      BasicFileAttributes attrs) throws IOException {
        if (file.toFile().getName().endsWith("String_Node_Str") || file.toFile().getName().endsWith("String_Node_Str")) {
          Path destinationFolder=destination.resolve(source.relativize(file.getParent()));
          if (!destinationFolder.toFile().exists() && !destinationFolder.toFile().mkdirs()) {
            System.err.printf("String_Node_Str",destinationFolder);
          }
          inOutMap.put(file,destinationFolder);
        }
        return CONTINUE;
      }
    }
);
  }
 else {
    inOutMap.put(source,destination);
  }
  for (  Map.Entry<Path,Path> inOut : inOutMap.entrySet()) {
    Path in=inOut.getKey();
    Path out=inOut.getValue();
    if (out.toFile().isDirectory()) {
      String name=in.toFile().getName();
      if (name.lastIndexOf('.') != -1) {
        name=name.substring(0,name.lastIndexOf('.'));
      }
switch (outputFormat) {
case JSON:
        name+="String_Node_Str";
      break;
case COFFEE:
    name+="String_Node_Str";
  break;
case XML:
default :
name+="String_Node_Str";
break;
}
out=out.resolve(name);
}
if (out.equals(in)) {
throw new IllegalArgumentException("String_Node_Str");
}
if (options.has(model)) {
final File modelFile=options.valueOf(model);
if (!modelFile.exists() || modelFile.isDirectory()) {
throw new IllegalArgumentException("String_Node_Str");
}
loadModelInfo(modelFile);
}
writeELM(in,out,outputFormat,options.has(optimization),options.has(annotations),options.has(verify));
}
}

Fixed version (ground truth):
public static void main(String[] args) throws IOException, InterruptedException {
  OptionParser parser=new OptionParser();
  OptionSpec<File> input=parser.accepts("String_Node_Str").withRequiredArg().ofType(File.class).required();
  OptionSpec<File> model=parser.accepts("String_Node_Str").withRequiredArg().ofType(File.class);
  OptionSpec<File> output=parser.accepts("String_Node_Str").withRequiredArg().ofType(File.class);
  OptionSpec<Format> format=parser.accepts("String_Node_Str").withRequiredArg().ofType(Format.class).defaultsTo(Format.XML);
  OptionSpec verify=parser.accepts("String_Node_Str");
  OptionSpec optimization=parser.accepts("String_Node_Str");
  OptionSpec annotations=parser.accepts("String_Node_Str");
  OptionSpec detailedErrors=parser.accepts("String_Node_Str");
  OptionSet options=parser.parse(args);
  final Path source=input.value(options).toPath();
  final Path destination=output.value(options) != null ? output.value(options).toPath() : source.toFile().isDirectory() ? source : source.getParent();
  final Format outputFormat=format.value(options);
  Map<Path,Path> inOutMap=new HashMap<>();
  if (source.toFile().isDirectory()) {
    if (destination.toFile().exists() && !destination.toFile().isDirectory()) {
      throw new IllegalArgumentException("String_Node_Str");
    }
    Files.walkFileTree(source,new SimpleFileVisitor<Path>(){
      @Override public FileVisitResult visitFile(      Path file,      BasicFileAttributes attrs) throws IOException {
        if (file.toFile().getName().endsWith("String_Node_Str") || file.toFile().getName().endsWith("String_Node_Str")) {
          Path destinationFolder=destination.resolve(source.relativize(file.getParent()));
          if (!destinationFolder.toFile().exists() && !destinationFolder.toFile().mkdirs()) {
            System.err.printf("String_Node_Str",destinationFolder);
          }
          inOutMap.put(file,destinationFolder);
        }
        return CONTINUE;
      }
    }
);
  }
 else {
    inOutMap.put(source,destination);
  }
  for (  Map.Entry<Path,Path> inOut : inOutMap.entrySet()) {
    Path in=inOut.getKey();
    Path out=inOut.getValue();
    if (out.toFile().isDirectory()) {
      String name=in.toFile().getName();
      if (name.lastIndexOf('.') != -1) {
        name=name.substring(0,name.lastIndexOf('.'));
      }
switch (outputFormat) {
case JSON:
        name+="String_Node_Str";
      break;
case COFFEE:
    name+="String_Node_Str";
  break;
case XML:
default :
name+="String_Node_Str";
break;
}
out=out.resolve(name);
}
if (out.equals(in)) {
throw new IllegalArgumentException("String_Node_Str");
}
if (options.has(model)) {
final File modelFile=options.valueOf(model);
if (!modelFile.exists() || modelFile.isDirectory()) {
throw new IllegalArgumentException("String_Node_Str");
}
loadModelInfo(modelFile);
}
writeELM(in,out,outputFormat,options.has(optimization),options.has(annotations),options.has(verify),options.has(detailedErrors));
}
}