Program: 151648
Project: 151648
Buggy source:
@DefaultCommand public void run(@Option(flagOnly=true,name="String_Node_Str",shortName="String_Node_Str",required=false) final boolean showAll,@Option(flagOnly=true,name="String_Node_Str",shortName="String_Node_Str",required=false) final boolean list,@Option(flagOnly=true,name="String_Node_Str",required=false) final boolean color,@Option(description="String_Node_Str",defaultValue="String_Node_Str") String... path){
  Map<String,List<String>> sortMap=new TreeMap<String,List<String>>();
  List<String> listBuild;
  List<String> coloredList=color ? new ArrayList<String>() : null;
  for (  String p : path) {
    Resource<?> resource=parsePathspec(factory,shell.getCurrentResource(),p);
    List<Resource<?>> childResources=resource.listResources();
    String el;
    File file;
    if (list) {
      int fileCount=0;
      boolean dir;
      for (      Resource<?> r : childResources) {
        sortMap.put(el=r.toString(),listBuild=new ArrayList<String>());
        file=(File)r.getUnderlyingResourceObject();
        dir=file.isDirectory();
        if (showAll || !el.startsWith("String_Node_Str")) {
          StringBuilder permissions=new StringBuilder(dir ? "String_Node_Str" : "String_Node_Str").append(file.canRead() ? 'r' : '-').append(file.canWrite() ? 'w' : '-').append(file.canExecute() ? 'x' : '-').append("String_Node_Str");
          listBuild.add(permissions.toString());
          listBuild.add("String_Node_Str");
          listBuild.add("String_Node_Str");
          listBuild.add(String.valueOf(file.length()));
          listBuild.addAll(Arrays.asList(getDateString(file.lastModified())));
          listBuild.add(el);
          if (!dir)           fileCount++;
        }
      }
      listBuild=new ArrayList<String>();
      for (      List<String> sublist : sortMap.values()) {
        listBuild.addAll(sublist);
      }
      shell.println("String_Node_Str" + fileCount);
      FormatCallback formatCallback=color ? new FormatCallback(){
        @Override public String format(        int column,        String value){
          if (column == 7 && value.endsWith("String_Node_Str"))           return shell.renderColor(ShellColor.BLUE,value);
          return value;
        }
      }
 : null;
      printOutTables(listBuild,new boolean[]{false,false,false,true,false,false,true,false},shell,formatCallback);
    }
 else {
      listBuild=new ArrayList<String>();
      for (      Resource<?> r : childResources) {
        el=r.toString();
        if (showAll || !el.startsWith("String_Node_Str")) {
          if (color) {
            coloredList.add(shell.renderColor(((FileResource)r).getUnderlyingResourceObject().isDirectory() ? ShellColor.BLUE : ShellColor.NONE,el));
          }
          listBuild.add(el);
        }
      }
      printOutColumns(listBuild,coloredList,shell,false);
    }
  }
}

Fixed version (ground truth):
@DefaultCommand public void run(@Option(flagOnly=true,name="String_Node_Str",shortName="String_Node_Str",required=false) final boolean showAll,@Option(flagOnly=true,name="String_Node_Str",shortName="String_Node_Str",required=false) final boolean list,@Option(flagOnly=true,name="String_Node_Str",required=false) final boolean color,@Option(description="String_Node_Str",defaultValue="String_Node_Str") String... path){
  Map<String,List<String>> sortMap=new TreeMap<String,List<String>>();
  List<String> listBuild;
  List<String> coloredList=color ? new ArrayList<String>() : null;
  for (  String p : path) {
    Resource<?> resource=parsePathspec(factory,shell.getCurrentResource(),p);
    List<Resource<?>> childResources=resource.listResources();
    String el;
    File file;
    if (list) {
      int fileCount=0;
      boolean dir;
      for (      Resource<?> r : childResources) {
        sortMap.put(el=r.toString(),listBuild=new ArrayList<String>());
        file=(File)r.getUnderlyingResourceObject();
        dir=file.isDirectory();
        if (showAll || !el.startsWith("String_Node_Str")) {
          StringBuilder permissions=new StringBuilder(dir ? "String_Node_Str" : "String_Node_Str").append(file.canRead() ? 'r' : '-').append(file.canWrite() ? 'w' : '-').append(file.canExecute() ? 'x' : '-').append("String_Node_Str");
          listBuild.add(permissions.toString());
          listBuild.add("String_Node_Str");
          listBuild.add("String_Node_Str");
          listBuild.add(String.valueOf(file.length()));
          listBuild.addAll(Arrays.asList(getDateString(file.lastModified())));
          listBuild.add(el);
          if (!dir)           fileCount++;
        }
      }
      listBuild=new ArrayList<String>();
      for (      List<String> sublist : sortMap.values()) {
        listBuild.addAll(sublist);
      }
      shell.println("String_Node_Str" + fileCount);
      FormatCallback formatCallback=color ? new FormatCallback(){
        @Override public String format(        int column,        String value){
          if (column == 7 && value.endsWith("String_Node_Str")) {
            return shell.renderColor(ShellColor.BLUE,value);
          }
 else {
            return value;
          }
        }
      }
 : null;
      printOutTables(listBuild,new boolean[]{false,false,false,true,false,false,true,false},shell,formatCallback);
    }
 else {
      listBuild=new ArrayList<String>();
      for (      Resource<?> r : childResources) {
        el=r.toString();
        if (showAll || !el.startsWith("String_Node_Str")) {
          if (color) {
            coloredList.add(shell.renderColor(((FileResource)r).getUnderlyingResourceObject().isDirectory() ? ShellColor.BLUE : ShellColor.NONE,el));
          }
          listBuild.add(el);
        }
      }
      printOutColumns(listBuild,coloredList,shell,false);
    }
  }
}