I got it working like this:
TestClass.Java
package classes;
public class TestClass {
public static void main(String[] args) {
System.out.println("Test");
}
}
Use javac on the command line to produce TestClass.class. Put TestClass.class in a folder classes/.
MANIFEST.MF
Manifest-Version: 1.0
Main-Class: classes.TestClass
Then run
jar cfm test.jar MANIFEST.MF classes/
Then run it as
java -jar test.jar