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Explode the two jars in the same folder, than remake a single jar out of them. Test. If it works (I guess it should), the problem is solved. Now just make sure that the MySQL license agreement allows this.
I know you said why you wanted everything in one jar, but why don't you want the user to have two jars in the folder? It's not like that would inconvenience the user in any way.
I'm very sure that what you are trying to achieve is against the licence agreement.
Also MySQL is not a free application when used as an embedded database.
>If you want to make it simple for the end-user, and your app. has a GUI, deploy it using webstart.
Is there a way to somehow include the MySQL connector in one of my JARs so that a user does not have to have two JARs in one folder for one program to run? >
A single link can take them to the 'download' page that uses [deployJava.js|http://java.sun.com/javase/6/docs/technotes/guides/jweb/deployment_advice.html] to check a suitable minimum version of Java is available before inserting the link to the launch/install file. If the user 'follows the prompts' from there, they might end up with a single menu item to launch the app., and no visible Jars.
I provide some [examples of the webstart API|http://pscode.org/jws/api.html] that show some services available to apps. launched using webstart, of particular use for your project might be the ExtensionInstallerService to install the DB, and the PersistenceService to store the path the user chose to install it (you would offer them the choice, of course).
Java webstart also offers other nice features like splash screens, icons..
Again, check the licensing arrangements - you might show the MySql license when installing.