Program: 3555
Project: 3555
Buggy source:
public static void main(String[] argv) throws Exception {
  System.setProperty("String_Node_Str","String_Node_Str");
  CommandLineParser parser=new PosixParser();
  int status=0;
  Options options=new Options();
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",true,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",true,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  OptionBuilder.withLongOpt("String_Node_Str");
  OptionBuilder.withValueSeparator(',');
  OptionBuilder.withDescription("String_Node_Str" + "String_Node_Str" + MEDIA_FILTER_PLUGINS_KEY + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str");
  Option pluginOption=OptionBuilder.create('p');
  pluginOption.setArgs(Option.UNLIMITED_VALUES);
  options.addOption(pluginOption);
  CommandLine line=null;
  try {
    line=parser.parse(options,argv);
  }
 catch (  MissingArgumentException e) {
    System.out.println("String_Node_Str" + e.getMessage());
    HelpFormatter myhelp=new HelpFormatter();
    myhelp.printHelp("String_Node_Str",options);
    System.exit(1);
  }
  if (line.hasOption('h')) {
    HelpFormatter myhelp=new HelpFormatter();
    myhelp.printHelp("String_Node_Str",options);
    System.exit(0);
  }
  if (line.hasOption('v')) {
    isVerbose=true;
  }
  if (line.hasOption('n')) {
    updateIndex=false;
  }
  if (line.hasOption('f')) {
    isForce=true;
  }
  if (line.hasOption('i')) {
    identifier=line.getOptionValue('i');
  }
  if (line.hasOption('m')) {
    max2Process=Integer.parseInt(line.getOptionValue('m'));
    if (max2Process <= 1) {
      System.out.println("String_Node_Str" + line.getOptionValue('m') + "String_Node_Str");
      max2Process=Integer.MAX_VALUE;
    }
  }
  String filterNames[]=null;
  if (line.hasOption('p')) {
    filterNames=line.getOptionValues('p');
    if (filterNames == null || filterNames.length == 0) {
      System.err.println("String_Node_Str" + "String_Node_Str");
      HelpFormatter myhelp=new HelpFormatter();
      myhelp.printHelp("String_Node_Str",options);
      System.exit(1);
    }
  }
 else {
    String enabledPlugins=ConfigurationManager.getProperty(MEDIA_FILTER_PLUGINS_KEY);
    filterNames=enabledPlugins.split("String_Node_Str");
  }
  List filterList=new ArrayList();
  for (int i=0; i < filterNames.length; i++) {
    FormatFilter filter=(FormatFilter)PluginManager.getNamedPlugin(FormatFilter.class,filterNames[i]);
    if (filter == null) {
      System.err.println("String_Node_Str" + filterNames[i] + "String_Node_Str");
      System.exit(1);
    }
 else {
      filterList.add(filter);
      String filterClassName=filter.getClass().getName();
      String pluginName=null;
      if (SelfNamedPlugin.class.isAssignableFrom(filter.getClass())) {
        pluginName=((SelfNamedPlugin)filter).getPluginInstanceName();
      }
      String formats=ConfigurationManager.getProperty(FILTER_PREFIX + "String_Node_Str" + filterClassName+ (pluginName != null ? "String_Node_Str" + pluginName : "String_Node_Str")+ "String_Node_Str"+ INPUT_FORMATS_SUFFIX);
      if (formats != null) {
        filterFormats.put(filterClassName + (pluginName != null ? FILTER_PLUGIN_SEPARATOR + pluginName : "String_Node_Str"),Arrays.asList(formats.split("String_Node_Str")));
      }
    }
  }
  if (isVerbose) {
    System.out.println("String_Node_Str");
    java.util.Iterator i=filterFormats.keySet().iterator();
    while (i.hasNext()) {
      String filterName=(String)i.next();
      System.out.println("String_Node_Str" + filterName);
      String pluginName=null;
      if (filterName.contains(FILTER_PLUGIN_SEPARATOR)) {
        String[] fields=filterName.split(FILTER_PLUGIN_SEPARATOR);
        filterName=fields[0];
        pluginName=fields[1];
      }
      System.out.println(filterName + (pluginName != null ? "String_Node_Str" + pluginName + "String_Node_Str" : "String_Node_Str"));
    }
  }
  filterClasses=(MediaFilter[])filterList.toArray(new MediaFilter[filterList.size()]);
  Context c=null;
  try {
    c=new Context();
    c.setIgnoreAuthorization(true);
    if (identifier == null) {
      applyFiltersAllItems(c);
    }
 else {
      DSpaceObject dso=HandleManager.resolveToObject(c,identifier);
      if (dso == null) {
        throw new IllegalArgumentException("String_Node_Str" + identifier + "String_Node_Str");
      }
switch (dso.getType()) {
case Constants.COMMUNITY:
        applyFiltersCommunity(c,(Community)dso);
      break;
case Constants.COLLECTION:
    applyFiltersCollection(c,(Collection)dso);
  break;
case Constants.ITEM:
applyFiltersItem(c,(Item)dso);
break;
}
}
if (updateIndex) {
System.out.println("String_Node_Str");
DSIndexer.updateIndex(c);
}
c.complete();
c=null;
}
 catch (Exception e) {
status=1;
}
 finally {
if (c != null) {
c.abort();
}
}
System.exit(status);
}

Fixed version (ground truth):
public static void main(String[] argv) throws Exception {
  System.setProperty("String_Node_Str","String_Node_Str");
  CommandLineParser parser=new PosixParser();
  int status=0;
  Options options=new Options();
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",true,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",true,"String_Node_Str");
  options.addOption("String_Node_Str","String_Node_Str",false,"String_Node_Str");
  OptionBuilder.withLongOpt("String_Node_Str");
  OptionBuilder.withValueSeparator(',');
  OptionBuilder.withDescription("String_Node_Str" + "String_Node_Str" + MEDIA_FILTER_PLUGINS_KEY + "String_Node_Str"+ "String_Node_Str"+ "String_Node_Str");
  Option pluginOption=OptionBuilder.create('p');
  pluginOption.setArgs(Option.UNLIMITED_VALUES);
  options.addOption(pluginOption);
  CommandLine line=null;
  try {
    line=parser.parse(options,argv);
  }
 catch (  MissingArgumentException e) {
    System.out.println("String_Node_Str" + e.getMessage());
    HelpFormatter myhelp=new HelpFormatter();
    myhelp.printHelp("String_Node_Str",options);
    System.exit(1);
  }
  if (line.hasOption('h')) {
    HelpFormatter myhelp=new HelpFormatter();
    myhelp.printHelp("String_Node_Str",options);
    System.exit(0);
  }
  if (line.hasOption('v')) {
    isVerbose=true;
  }
  if (line.hasOption('n')) {
    updateIndex=false;
  }
  if (line.hasOption('f')) {
    isForce=true;
  }
  if (line.hasOption('i')) {
    identifier=line.getOptionValue('i');
  }
  if (line.hasOption('m')) {
    max2Process=Integer.parseInt(line.getOptionValue('m'));
    if (max2Process <= 1) {
      System.out.println("String_Node_Str" + line.getOptionValue('m') + "String_Node_Str");
      max2Process=Integer.MAX_VALUE;
    }
  }
  String filterNames[]=null;
  if (line.hasOption('p')) {
    filterNames=line.getOptionValues('p');
    if (filterNames == null || filterNames.length == 0) {
      System.err.println("String_Node_Str" + "String_Node_Str");
      HelpFormatter myhelp=new HelpFormatter();
      myhelp.printHelp("String_Node_Str",options);
      System.exit(1);
    }
  }
 else {
    String enabledPlugins=ConfigurationManager.getProperty(MEDIA_FILTER_PLUGINS_KEY);
    filterNames=enabledPlugins.split("String_Node_Str");
  }
  List filterList=new ArrayList();
  for (int i=0; i < filterNames.length; i++) {
    FormatFilter filter=(FormatFilter)PluginManager.getNamedPlugin(FormatFilter.class,filterNames[i]);
    if (filter == null) {
      System.err.println("String_Node_Str" + filterNames[i] + "String_Node_Str");
      System.exit(1);
    }
 else {
      filterList.add(filter);
      String filterClassName=filter.getClass().getName();
      String pluginName=null;
      if (SelfNamedPlugin.class.isAssignableFrom(filter.getClass())) {
        pluginName=((SelfNamedPlugin)filter).getPluginInstanceName();
      }
      String formats=ConfigurationManager.getProperty(FILTER_PREFIX + "String_Node_Str" + filterClassName+ (pluginName != null ? "String_Node_Str" + pluginName : "String_Node_Str")+ "String_Node_Str"+ INPUT_FORMATS_SUFFIX);
      if (formats != null) {
        filterFormats.put(filterClassName + (pluginName != null ? FILTER_PLUGIN_SEPARATOR + pluginName : "String_Node_Str"),Arrays.asList(formats.split("String_Node_Str")));
      }
    }
  }
  if (isVerbose) {
    System.out.println("String_Node_Str");
    java.util.Iterator i=filterFormats.keySet().iterator();
    while (i.hasNext()) {
      String filterName=(String)i.next();
      System.out.println("String_Node_Str" + filterName);
      String pluginName=null;
      if (filterName.contains(FILTER_PLUGIN_SEPARATOR)) {
        String[] fields=filterName.split(FILTER_PLUGIN_SEPARATOR);
        filterName=fields[0];
        pluginName=fields[1];
      }
      System.out.println(filterName + (pluginName != null ? "String_Node_Str" + pluginName + "String_Node_Str" : "String_Node_Str"));
    }
  }
  filterClasses=(FormatFilter[])filterList.toArray(new FormatFilter[filterList.size()]);
  Context c=null;
  try {
    c=new Context();
    c.setIgnoreAuthorization(true);
    if (identifier == null) {
      applyFiltersAllItems(c);
    }
 else {
      DSpaceObject dso=HandleManager.resolveToObject(c,identifier);
      if (dso == null) {
        throw new IllegalArgumentException("String_Node_Str" + identifier + "String_Node_Str");
      }
switch (dso.getType()) {
case Constants.COMMUNITY:
        applyFiltersCommunity(c,(Community)dso);
      break;
case Constants.COLLECTION:
    applyFiltersCollection(c,(Collection)dso);
  break;
case Constants.ITEM:
applyFiltersItem(c,(Item)dso);
break;
}
}
if (updateIndex) {
System.out.println("String_Node_Str");
DSIndexer.updateIndex(c);
}
c.complete();
c=null;
}
 catch (Exception e) {
status=1;
}
 finally {
if (c != null) {
c.abort();
}
}
System.exit(status);
}