If it's in the classpath, it should work correctly. I am not quite sure where you have set the Add external file option.
You have an alternative: In the new version of the tools (3.2.0 beta 9 - the one you are using), you can set the option to include the project's default classpath.
In the Hibernate Configurations view change to the Classpath tab and click the checkbox at the bottom: Include default classpath from project. If you have configured the MySQL drivers correctly in Eclipse, it should work.
Hope this could help you,
Kariem
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