Inside my jar file I had a folder called Upload, this folder had three other text files inside it and I needed to have an exactly the same folder and files outside of the jar file, I used the code below:
URL inputUrl = getClass().getResource("/upload/blabla1.txt");
File dest1 = new File("upload/blabla1.txt");
FileUtils.copyURLToFile(inputUrl, dest1);
URL inputUrl2 = getClass().getResource("/upload/blabla2.txt");
File dest2 = new File("upload/blabla2.txt");
FileUtils.copyURLToFile(inputUrl2, dest2);
URL inputUrl3 = getClass().getResource("/upload/blabla3.txt");
File dest3 = new File("upload/Bblabla3.txt");
FileUtils.copyURLToFile(inputUrl3, dest3);