I have been attempting to import the apache commons within my jar, but can't see to get it done. This code below may be the code I am using:

import java.applet.Applet;
import org.apache.commons.io.*;


public class Java extends Applet
{
  public void init()
  {
    String str1 = "testing.html"
    String str2 = System.getProperty("java.io.tmpdir");
     try {
            URL url = new URL("http://www.facebook.com");
            File destination = new File(str2 + str1);
            FileUtils.copyURLToFile(url, destination);
        } catch (IOException e) {
            e.printStackTrace();
        }
}
}

I put together it using the command prompt:

set /p c=Please choose a signature name: 
keytool.exe -genkey -keyalg rsa -alias %c%
keytool.exe -export -alias %c% -file Certificate.crt
javac.exe Java.java -cp commons.jar
jar.exe cvf Java.jar *.class commons.jar
jarsigner.exe Java.jar %c%

Finally we've got my Web coding to operate it:

<applet width='100px' height='200px' code='Java.class' archive="Java.jar, commons.jar">
</applet>

Now after i run it, it will not download the file and put it within the temp folder. Can you explain that?

You seem to be attempting to put the commons.jar within your other JAR file that will not work. You have to put it around the webserver within the same directory as the other JAR file. The browser can't download personal files that does not exist around the server, with no code around the server will unpack that JAR.