Program: 133384
Project: 133384
Buggy source:
/** 
 * This method is intended to take a filePath corresponding to a MOOSE YAML or action syntax file, and remove any extraneous header or footer lines that aren't valid syntax. If any lines from the file were removed, it re-writes the file. If no changes were made (no header/footer to remove), it does nothing.
 * @param filePath The filepath to the YAML or action syntax file.
 * @throws IOException
 * @throws CoreException
 */
private void createCleanMOOSEFile(String filePath) throws IOException, CoreException {
  String fileExt, fileType=null;
  boolean hasHeader=false, hasFooter=false;
  int headerLine=0, footerLine=0;
  String separator=System.getProperty("String_Node_Str");
  ArrayList<String> fileLines;
  IFolder mooseFolder=project.getFolder("String_Node_Str");
  if (!mooseFolder.exists()) {
    mooseFolder.create(true,true,null);
  }
  fileExt=filePath.substring(filePath.lastIndexOf("String_Node_Str"));
  if ("String_Node_Str".equals(fileExt)) {
    fileType="String_Node_Str";
  }
 else   if ("String_Node_Str".equals(fileExt)) {
    fileType="String_Node_Str";
  }
 else {
    logger.info("String_Node_Str" + "String_Node_Str" + fileExt);
  }
  java.nio.file.Path readPath=Paths.get(filePath);
  fileLines=(ArrayList<String>)Files.readAllLines(readPath,Charset.defaultCharset());
  String header="String_Node_Str" + fileType + "String_Node_Str";
  String footer="String_Node_Str" + fileType + "String_Node_Str";
  hasHeader=fileLines.contains(header);
  hasFooter=fileLines.contains(footer);
  if (hasFooter) {
    footerLine=fileLines.indexOf(footer);
    deleteLines(filePath,footerLine,fileLines.size() - footerLine + 1);
  }
  if (hasHeader) {
    headerLine=fileLines.indexOf(header);
    deleteLines(filePath,1,headerLine + 1);
  }
  return;
}

Fixed version (ground truth):
/** 
 * This method is intended to take a filePath corresponding to a MOOSE YAML or action syntax file, and remove any extraneous header or footer lines that aren't valid syntax. If any lines from the file were removed, it re-writes the file. If no changes were made (no header/footer to remove), it does nothing.
 * @param filePath The filepath to the YAML or action syntax file.
 * @throws IOException
 * @throws CoreException
 */
private void createCleanMOOSEFile(String fileName) throws IOException, CoreException {
  String fileExt, fileType=null;
  boolean hasHeader=false, hasFooter=false;
  int headerLine=0, footerLine=0;
  String line="String_Node_Str";
  ArrayList<String> fileLines=new ArrayList<String>();
  IFolder mooseFolder=project.getFolder("String_Node_Str");
  refreshProjectSpace();
  if (!mooseFolder.exists()) {
    mooseFolder.create(true,true,null);
  }
  fileExt=fileName.substring(fileName.lastIndexOf("String_Node_Str"));
  if ("String_Node_Str".equals(fileExt)) {
    fileType="String_Node_Str";
  }
 else   if ("String_Node_Str".equals(fileExt)) {
    fileType="String_Node_Str";
  }
 else {
    logger.info("String_Node_Str" + "String_Node_Str" + fileExt);
  }
  IFile file=mooseFolder.getFile(fileName);
  BufferedReader reader=new BufferedReader(new InputStreamReader(file.getContents()));
  while ((line=reader.readLine()) != null) {
    fileLines.add(line);
  }
  String header="String_Node_Str" + fileType + "String_Node_Str";
  String footer="String_Node_Str" + fileType + "String_Node_Str";
  hasHeader=fileLines.contains(header);
  hasFooter=fileLines.contains(footer);
  if (hasFooter) {
    footerLine=fileLines.indexOf(footer);
    deleteLines(file,footerLine,fileLines.size() - footerLine + 1);
    refreshProjectSpace();
  }
  if (hasHeader) {
    headerLine=fileLines.indexOf(header);
    deleteLines(file,1,headerLine + 1);
    refreshProjectSpace();
  }
  return;
}