Program: 37668
Project: 37668
Buggy source:
static boolean assemble(){
  try {
    Simulator.kill();
    if (AssemblerOptions.tape && AssemblerOptions.tapeEncoding && !AssemblerOptions.tapeEncodingChoice.equals(AssemblerOptions.deckEncodingChoice)) {
      String[] tapeArgs=buildCommand(false).toArray(new String[0]);
      process=Runtime.getRuntime().exec(tapeArgs);
      stdout=new BufferedReader(new InputStreamReader(process.getInputStream()));
      try {
        process.waitFor();
      }
 catch (      Exception ex) {
      }
      if (AssemblerOptions.tape && AssemblerOptions.convertTapeForTapeSimulator) {
        convertTape(AssemblerOptions.tapePath);
      }
      String[] deckArgs=buildCommand(true).toArray(new String[0]);
      process=Runtime.getRuntime().exec(deckArgs);
      stdout=new BufferedReader(new InputStreamReader(process.getInputStream()));
    }
 else {
      String[] args=AssemblerOptions.command.toArray(new String[0]);
      args[0]=AssemblerOptions.assemblerPath;
      process=Runtime.getRuntime().exec(args);
      stdout=new BufferedReader(new InputStreamReader(process.getInputStream()));
      if (AssemblerOptions.tape && AssemblerOptions.convertTapeForTapeSimulator) {
        try {
          process.waitFor();
        }
 catch (        Exception ex) {
        }
        convertTape(AssemblerOptions.tapePath);
      }
    }
    process=null;
    return true;
  }
 catch (  IOException ex) {
    ex.printStackTrace();
    return false;
  }
}

Fixed version (ground truth):
static boolean assemble(){
  try {
    Simulator.kill();
    new File(AssemblerOptions.objectPath).delete();
    new File(AssemblerOptions.tapePath).delete();
    new File(AssemblerOptions.diagnosticPath).delete();
    new File(AssemblerOptions.listingPath).delete();
    new File(RopeUtils.removeExtension(AssemblerOptions.sourcePath) + "String_Node_Str").delete();
    if (AssemblerOptions.tape && AssemblerOptions.tapeEncoding && !AssemblerOptions.tapeEncodingChoice.equals(AssemblerOptions.deckEncodingChoice)) {
      String[] tapeArgs=buildCommand(false).toArray(new String[0]);
      process=Runtime.getRuntime().exec(tapeArgs);
      stdout=new BufferedReader(new InputStreamReader(process.getInputStream()));
      try {
        process.waitFor();
      }
 catch (      Exception ex) {
      }
      if (AssemblerOptions.tape && AssemblerOptions.convertTapeForTapeSimulator) {
        convertTape(AssemblerOptions.tapePath);
      }
      String[] deckArgs=buildCommand(true).toArray(new String[0]);
      process=Runtime.getRuntime().exec(deckArgs);
      stdout=new BufferedReader(new InputStreamReader(process.getInputStream()));
    }
 else {
      String[] args=AssemblerOptions.command.toArray(new String[0]);
      args[0]=AssemblerOptions.assemblerPath;
      process=Runtime.getRuntime().exec(args);
      stdout=new BufferedReader(new InputStreamReader(process.getInputStream()));
      if (AssemblerOptions.tape && AssemblerOptions.convertTapeForTapeSimulator) {
        try {
          process.waitFor();
        }
 catch (        Exception ex) {
        }
        convertTape(AssemblerOptions.tapePath);
      }
    }
    process=null;
    return true;
  }
 catch (  IOException ex) {
    ex.printStackTrace();
    return false;
  }
}