Program: 58273
Project: 58273
Buggy source:
@Override public Boolean call() throws Exception {
  LOG.log(Level.INFO,"String_Node_Str");
  FileObject fileObject=dataObject.getPrimaryFile();
  String oldContent=getFileContent(fileObject);
  EditorCookie cookie=getEditorCookie(fileObject);
  boolean isOpenedInEditor=cookie != null && cookie.getDocument() != null;
  if (isOpenedInEditor) {
    LOG.log(Level.INFO,"String_Node_Str");
    MultipleFileWritesUITask action=new MultipleFileWritesUITask(fileObject,cookie,lineEnding,finalnewline,trimwhitespace);
    WindowManager.getDefault().invokeWhenUIReady(action);
  }
 else {
    String content=oldContent;
    LOG.log(Level.INFO,"String_Node_Str");
    if (finalnewline) {
      LOG.log(Level.INFO,"String_Node_Str");
      String tempContent=content;
      content=finalNewline(content,lineEnding);
      if (tempContent.equals(content)) {
        LOG.log(Level.INFO,"String_Node_Str");
        finalnewline=false;
      }
 else {
        LOG.log(Level.INFO,"String_Node_Str");
      }
    }
    if (trimwhitespace) {
      LOG.log(Level.INFO,"String_Node_Str");
      String tempContent=content;
      content=trimWhitespaces(content,lineEnding);
      if (tempContent.equals(content)) {
        LOG.log(Level.INFO,"String_Node_Str");
        trimwhitespace=false;
      }
 else {
        LOG.log(Level.INFO,"String_Node_Str");
      }
    }
    if (!finalnewline && !trimwhitespace) {
      charsetIfChanged(fileObject,content,charset);
    }
 else {
      charset(fileObject,content,charset);
    }
  }
  return true;
}

Fixed version (ground truth):
@Override public Boolean call() throws Exception {
  LOG.log(Level.INFO,"String_Node_Str");
  FileObject fileObject=dataObject.getPrimaryFile();
  String oldContent=getFileContent(fileObject);
  EditorCookie cookie=getEditorCookie(fileObject);
  boolean isOpenedInEditor=cookie != null && cookie.getDocument() != null;
  if (isOpenedInEditor) {
    LOG.log(Level.INFO,"String_Node_Str");
    MultipleFileWritesUITask action=new MultipleFileWritesUITask(fileObject,cookie,lineEnding,finalnewline,trimwhitespace);
    WindowManager.getDefault().invokeWhenUIReady(action);
  }
 else {
    String content=oldContent;
    LOG.log(Level.INFO,"String_Node_Str");
    if (trimwhitespace) {
      LOG.log(Level.INFO,"String_Node_Str");
      String tempContent=content;
      LOG.log(Level.INFO,"String_Node_Str",tempContent);
      content=trimWhitespaces(content,lineEnding);
      if (tempContent.endsWith("String_Node_Str") || tempContent.endsWith("String_Node_Str")) {
        content=content + lineEnding;
      }
      if (tempContent.equals(content)) {
        LOG.log(Level.INFO,"String_Node_Str");
        trimwhitespace=false;
      }
 else {
        LOG.log(Level.INFO,"String_Node_Str");
      }
      LOG.log(Level.INFO,"String_Node_Str",content);
    }
    if (finalnewline) {
      LOG.log(Level.INFO,"String_Node_Str");
      String tempContent=content;
      LOG.log(Level.INFO,"String_Node_Str",tempContent);
      content=finalNewline(content,lineEnding);
      if (tempContent.equals(content)) {
        LOG.log(Level.INFO,"String_Node_Str");
        finalnewline=false;
      }
 else {
        LOG.log(Level.INFO,"String_Node_Str");
      }
      LOG.log(Level.INFO,"String_Node_Str",content);
    }
    if (!finalnewline && !trimwhitespace) {
      charsetIfChanged(fileObject,content,charset);
    }
 else {
      charset(fileObject,content,charset);
    }
  }
  return true;
}