I have been searching for a solution for this issue for multiple hours today and many hours yesterday so I decided to address it here, although it seems a stupid issue.
this solution that:
You still need to add the jar files to the java build path to avoid compilation errors after adding the files to the war/WEB-INF/lib folder!
Might be "a little" too late for this, but in eclipse you don't have to manually copy. Right-Click on project -> Build Path -> Configure Build Path... -> select Deployment Assembly (left). Add your jars here and they will be included when deploying.
Copy paste the .jar files to war/WEB-INF/lib and then go to Properties(of the project in Eclipse) --> Java Build Path --> Add JARs --> Select the related .jars from the current project. You should be all set!
You are on the right track. Since the app when deployed to appengine is packaged as a war (web application archive), library jars need to be in WEB-INF/lib. You should ensure your jars are there and then add those jars to your eclipse build path. Try doing a "clean" operation on the project and re-building it to ensure the libraries is in the package.