I am unable to see the relattionship when using Mysql with Middlegen-hibernate r-4 version with mysql-4.1.1a-alpha and three different jdbc drivers (mysql-connector-java-3.1.1-alpha,mysql-connector-java-3.0.11-stable,mysql-connector-java-3.0.10-stable)

I also double checked if the tables have relataionship, the two tables have the following relataionship:
ALTER TABLE lineitem ADD CONSTRAINT fk_lineitem_orders FOREIGN KEY(orderid) REFERENCES orders (orderid) ON DELETE NO ACTION ON UPDATE NO ACTION;

Anyone has any idea what I am doing wrong.

I can see you have tried a few JDBC drivers. In my experience is almost always the driver and usually on the latest stable driver for the DB version operates the best.
It is the driver that provides the meta data so that the tables and relationships are present. Check that your constraints are in place and correct . The try the JDBC Driver(s) where maybe you will need to code a small Meta data testing program to see what is being returned.

I figured out the problem after carefully reading Mysql manual that I need indexes for the relationships to work.

Thanks for providing the solution discovered for your question. I will put the answer into the back of my mind as a suggestion for the future.