Program: 100906
Project: 100906
Buggy source:
/** 
 * Parses the command line arguments and provides feedback to the main class.
 * @return A boolean value if there is a file to be processed by arara.
 */
public boolean parse(){
  Option optVersion=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optHelp=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optLog=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optVerbose=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optTimeout=new Option("String_Node_Str","String_Node_Str",true,localization.getMessage("String_Node_Str"));
  Option optLanguage=new Option("String_Node_Str","String_Node_Str",true,localization.getMessage("String_Node_Str"));
  Option optDryRun=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optMaxNumberLoops=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  commandLineOptions.addOption(optVersion);
  commandLineOptions.addOption(optHelp);
  commandLineOptions.addOption(optLog);
  commandLineOptions.addOption(optVerbose);
  commandLineOptions.addOption(optTimeout);
  commandLineOptions.addOption(optLanguage);
  commandLineOptions.addOption(optDryRun);
  commandLineOptions.addOption(optMaxNumberLoops);
  CommandLineParser parser=new BasicParser();
  try {
    CommandLine line=parser.parse(commandLineOptions,theArgs);
    if (line.hasOption("String_Node_Str")) {
      LanguageController language=new LanguageController();
      if (!language.setLanguage(line.getOptionValue("String_Node_Str"))) {
        language.printLanguageHelp();
        printUsage();
        return false;
      }
 else {
        optVersion.setDescription(localization.getMessage("String_Node_Str"));
        optHelp.setDescription(localization.getMessage("String_Node_Str"));
        optLog.setDescription(localization.getMessage("String_Node_Str"));
        optVerbose.setDescription(localization.getMessage("String_Node_Str"));
        optTimeout.setDescription(localization.getMessage("String_Node_Str"));
        optLanguage.setDescription(localization.getMessage("String_Node_Str"));
        optDryRun.setDescription(localization.getMessage("String_Node_Str"));
        optMaxNumberLoops.setDescription(localization.getMessage("String_Node_Str"));
      }
    }
    if (line.hasOption("String_Node_Str")) {
      printVersion();
      printUsage();
      return false;
    }
 else {
      if (line.hasOption("String_Node_Str")) {
        printVersion();
        printSpecialThanks();
        return false;
      }
 else {
        String[] files=line.getArgs();
        if (files.length != 1) {
          printVersion();
          printUsage();
          return false;
        }
 else {
          if (line.hasOption("String_Node_Str")) {
            try {
              executionTimeout=Long.parseLong(line.getOptionValue("String_Node_Str"));
              if (executionTimeout <= 0) {
                printVersion();
                printUsage();
                return false;
              }
            }
 catch (            NumberFormatException numberFormatException) {
              printVersion();
              printUsage();
              return false;
            }
          }
 else {
            executionTimeout=0;
          }
          if (line.hasOption("String_Node_Str")) {
            try {
              maximumNumberOfLoops=Long.parseLong(line.getOptionValue("String_Node_Str"));
              if (maximumNumberOfLoops <= 0) {
                printVersion();
                printUsage();
                return false;
              }
            }
 catch (            NumberFormatException numberFormatException) {
              printVersion();
              printUsage();
              return false;
            }
          }
 else {
            maximumNumberOfLoops=AraraConstants.MAXLOOPS;
          }
          AraraLogging.enableLogging(line.hasOption("String_Node_Str"));
          showVerboseOutput=line.hasOption("String_Node_Str");
          if (line.hasOption("String_Node_Str")) {
            showVerboseOutput=false;
            dryRun=true;
          }
          theFile=files[0];
          if (!checkFile(theFile,configuration.getValidExtensions())) {
            return false;
          }
          return true;
        }
      }
    }
  }
 catch (  ParseException parseException) {
    printVersion();
    printUsage();
    return false;
  }
}

Fixed version (ground truth):
/** 
 * Parses the command line arguments and provides feedback to the main class.
 * @return A boolean value if there is a file to be processed by arara.
 */
public boolean parse(){
  Option optVersion=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optHelp=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optLog=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optVerbose=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optTimeout=new Option("String_Node_Str","String_Node_Str",true,localization.getMessage("String_Node_Str"));
  Option optLanguage=new Option("String_Node_Str","String_Node_Str",true,localization.getMessage("String_Node_Str"));
  Option optDryRun=new Option("String_Node_Str","String_Node_Str",false,localization.getMessage("String_Node_Str"));
  Option optMaxNumberLoops=new Option("String_Node_Str","String_Node_Str",true,localization.getMessage("String_Node_Str"));
  commandLineOptions.addOption(optVersion);
  commandLineOptions.addOption(optHelp);
  commandLineOptions.addOption(optLog);
  commandLineOptions.addOption(optVerbose);
  commandLineOptions.addOption(optTimeout);
  commandLineOptions.addOption(optLanguage);
  commandLineOptions.addOption(optDryRun);
  commandLineOptions.addOption(optMaxNumberLoops);
  CommandLineParser parser=new BasicParser();
  try {
    CommandLine line=parser.parse(commandLineOptions,theArgs);
    if (line.hasOption("String_Node_Str")) {
      LanguageController language=new LanguageController();
      if (!language.setLanguage(line.getOptionValue("String_Node_Str"))) {
        language.printLanguageHelp();
        printUsage();
        return false;
      }
 else {
        optVersion.setDescription(localization.getMessage("String_Node_Str"));
        optHelp.setDescription(localization.getMessage("String_Node_Str"));
        optLog.setDescription(localization.getMessage("String_Node_Str"));
        optVerbose.setDescription(localization.getMessage("String_Node_Str"));
        optTimeout.setDescription(localization.getMessage("String_Node_Str"));
        optLanguage.setDescription(localization.getMessage("String_Node_Str"));
        optDryRun.setDescription(localization.getMessage("String_Node_Str"));
        optMaxNumberLoops.setDescription(localization.getMessage("String_Node_Str"));
      }
    }
    if (line.hasOption("String_Node_Str")) {
      printVersion();
      printUsage();
      return false;
    }
 else {
      if (line.hasOption("String_Node_Str")) {
        printVersion();
        printSpecialThanks();
        return false;
      }
 else {
        String[] files=line.getArgs();
        if (files.length != 1) {
          printVersion();
          printUsage();
          return false;
        }
 else {
          if (line.hasOption("String_Node_Str")) {
            try {
              executionTimeout=Long.parseLong(line.getOptionValue("String_Node_Str"));
              if (executionTimeout <= 0) {
                printVersion();
                printUsage();
                return false;
              }
            }
 catch (            NumberFormatException numberFormatException) {
              printVersion();
              printUsage();
              return false;
            }
          }
 else {
            executionTimeout=0;
          }
          if (line.hasOption("String_Node_Str")) {
            try {
              maximumNumberOfLoops=Long.parseLong(line.getOptionValue("String_Node_Str"));
              if (maximumNumberOfLoops <= 0) {
                printVersion();
                printUsage();
                return false;
              }
            }
 catch (            NumberFormatException numberFormatException) {
              printVersion();
              printUsage();
              return false;
            }
          }
 else {
            maximumNumberOfLoops=AraraConstants.MAXLOOPS;
          }
          AraraLogging.enableLogging(line.hasOption("String_Node_Str"));
          showVerboseOutput=line.hasOption("String_Node_Str");
          if (line.hasOption("String_Node_Str")) {
            showVerboseOutput=false;
            dryRun=true;
          }
          theFile=files[0];
          if (!checkFile(theFile,configuration.getValidExtensions())) {
            return false;
          }
          return true;
        }
      }
    }
  }
 catch (  ParseException parseException) {
    printVersion();
    printUsage();
    return false;
  }
}