Program: 100907
Project: 100907
Buggy source:
/** 
 * The main method. The idea is to provide to arara only the supported file name and let it handle. The application will remove the file extension (if any) and call the other helper classes.
 * @param args The command line arguments. In fact, arara supports a lot offlags, all listed in the CommandLineAnalyzer.
 */
public static void main(String[] args){
  int exitStatus;
  try {
    AraraUtils.printHeader();
    ConfigurationLoader configuration=new ConfigurationLoader();
    configuration.load();
    CommandLineAnalyzer commandLine=new CommandLineAnalyzer(args,configuration);
    if (!commandLine.parse()) {
      exitStatus=0;
      System.exit(exitStatus);
    }
    File file;
    file=new File(commandLine.getFile());
    logger.info(localization.getMessage("String_Node_Str"));
    logger.info(localization.getMessage("String_Node_Str",file.getName()));
    DirectiveExtractor dirExtractor=new DirectiveExtractor(file,configuration);
    dirExtractor.extract();
    DirectiveParser dirParser=new DirectiveParser(dirExtractor.getDirectives());
    file=commandLine.getFileReference();
    dirParser.setFile(file);
    TaskDeployer taskDeployer=new TaskDeployer(dirParser.parse(),configuration);
    CommandTrigger commandTrigger=new CommandTrigger(taskDeployer.deploy());
    commandTrigger.setVerbose(commandLine.isVerbose());
    commandTrigger.setExecutionTimeout(commandLine.getExecutionTimeout());
    boolean overallResult=commandTrigger.execute();
    logger.info(localization.getMessage("String_Node_Str"));
    if (overallResult) {
      exitStatus=0;
    }
 else {
      exitStatus=1;
    }
  }
 catch (  Exception exception) {
    System.out.println(AraraUtils.wrap(exception.getMessage()));
    logger.error(localization.getMessage("String_Node_Str"));
    logger.error(exception.getMessage());
    exitStatus=1;
  }
  System.exit(exitStatus);
}

Fixed version (ground truth):
/** 
 * The main method. The idea is to provide to arara only the supported file name and let it handle. The application will remove the file extension (if any) and call the other helper classes.
 * @param args The command line arguments. In fact, arara supports a lot offlags, all listed in the CommandLineAnalyzer.
 */
public static void main(String[] args){
  int exitStatus;
  try {
    AraraUtils.printHeader();
    ConfigurationLoader configuration=new ConfigurationLoader();
    configuration.load();
    CommandLineAnalyzer commandLine=new CommandLineAnalyzer(args,configuration);
    if (!commandLine.parse()) {
      exitStatus=0;
      System.exit(exitStatus);
    }
    File file;
    file=new File(commandLine.getFile());
    logger.info(localization.getMessage("String_Node_Str"));
    logger.info(localization.getMessage("String_Node_Str",file.getName()));
    DirectiveExtractor dirExtractor=new DirectiveExtractor(file,configuration);
    dirExtractor.extract();
    DirectiveParser dirParser=new DirectiveParser(dirExtractor.getDirectives());
    dirParser.setFile(file);
    TaskDeployer taskDeployer=new TaskDeployer(dirParser.parse(),configuration);
    CommandTrigger commandTrigger=new CommandTrigger(taskDeployer.deploy());
    commandTrigger.setVerbose(commandLine.isVerbose());
    commandTrigger.setExecutionTimeout(commandLine.getExecutionTimeout());
    boolean overallResult=commandTrigger.execute();
    logger.info(localization.getMessage("String_Node_Str"));
    if (overallResult) {
      exitStatus=0;
    }
 else {
      exitStatus=1;
    }
  }
 catch (  Exception exception) {
    System.out.println(AraraUtils.wrap(exception.getMessage()));
    logger.error(localization.getMessage("String_Node_Str"));
    logger.error(exception.getMessage());
    exitStatus=1;
  }
  System.exit(exitStatus);
}