VFS из Linux Kernel и Apache Commons VFS

import java.nio.file.*;

public class Main {
   public static void main(String[] args) throws Exception {
       Path lowerDir = Paths.get("/path/to/lower");
       Path upperDir = Paths.get("/path/to/upper");
       Path workDir = Paths.get("/path/to/work");
       Path mergedDir = Paths.get("/path/to/merged");

       // Создаем рабочий каталог
       Files.createDirectories(workDir);

       // Монтируем overlayfs
       String[] mountOptions = {"lowerdir=" + lowerDir.toString(), "upperdir=" + upperDir.toString(), "workdir=" + workDir.toString()};
       Filesystems.newFileSystem(URI.create("overlay:" + mergedDir.toString()), Collections.emptyMap());
   }
}