Program: 37657
Project: 37657
Buggy source:
String cleanupSource(String source,Boolean removedInvalidChars) throws Exception {
  removedInvalidChars=false;
  if (source.isEmpty()) {
    return source.concat("String_Node_Str");
  }
  String timeID=getTimeID();
  int lastChIdx=source.length() - 1;
  if (source.charAt(lastChIdx) != '\n') {
    source=source.concat("String_Node_Str");
  }
 else {
    int removedNewlines=0;
    while (lastChIdx >= 1) {
      Character ch1=source.charAt(lastChIdx);
      if (ch1 == '\n' || Character.isWhitespace(ch1)) {
        source=source.substring(0,lastChIdx--);
        removedNewlines++;
      }
 else {
        break;
      }
    }
    removedInvalidChars=(removedNewlines > 1);
    source=source.concat("String_Node_Str");
  }
  boolean jobCardModified=false;
  List<String> lines=new ArrayList<>();
  try (BufferedReader reader=new BufferedReader(new StringReader(source))){
    String line;
    while ((line=reader.readLine()) != null) {
      if (line.length() >= 18 && line.substring(15,18).compareTo("String_Node_Str") == 0) {
        if (line.length() < 75) {
          line=String.format("String_Node_Str",line);
        }
 else         if (line.length() > 75) {
          line=line.substring(0,75);
        }
        line=line.concat(timeID);
        System.out.println("String_Node_Str" + timeID + "String_Node_Str"+ baseName+ "String_Node_Str"+ fileExt);
        jobCardModified=true;
      }
      lines.add(line);
    }
  }
   if (jobCardModified) {
    StringWriter writer=new StringWriter();
    for (    String line : lines) {
      writer.write(line + "String_Node_Str");
    }
    source=writer.toString();
  }
  return source;
}

Fixed version (ground truth):
String cleanupSource(String source,BoolRef removedInvalidChars) throws Exception {
  removedInvalidChars.value=false;
  if (source.isEmpty()) {
    return source.concat("String_Node_Str");
  }
  String timeID=getTimeID();
  int lastChIdx=source.length() - 1;
  if (source.charAt(lastChIdx) != '\n') {
    source=source.concat("String_Node_Str");
  }
 else {
    int removedNewlines=0;
    while (lastChIdx >= 1) {
      Character ch1=source.charAt(lastChIdx);
      if (ch1 == '\n' || Character.isWhitespace(ch1)) {
        source=source.substring(0,lastChIdx--);
        removedNewlines++;
      }
 else {
        break;
      }
    }
    removedInvalidChars.value=(removedNewlines > 1);
    source=source.concat("String_Node_Str");
  }
  boolean jobCardModified=false;
  List<String> lines=new ArrayList<>();
  try (BufferedReader reader=new BufferedReader(new StringReader(source))){
    String line;
    while ((line=reader.readLine()) != null) {
      if (line.length() >= 18 && line.substring(15,18).compareTo("String_Node_Str") == 0) {
        if (line.length() < 75) {
          line=String.format("String_Node_Str",line);
        }
 else         if (line.length() > 75) {
          line=line.substring(0,75);
        }
        line=line.concat(timeID);
        System.out.println("String_Node_Str" + timeID + "String_Node_Str"+ baseName+ "String_Node_Str"+ fileExt);
        jobCardModified=true;
      }
      lines.add(line);
    }
  }
   if (jobCardModified) {
    StringWriter writer=new StringWriter();
    for (    String line : lines) {
      writer.write(line + "String_Node_Str");
    }
    source=writer.toString();
  }
  return source;
}