I am creating an application that runs downloaded Java code, and I would like to be able to specify exactly which built-in Java classes the code can access. I imagine this involves using a ClassLoader and SecurityManager, but what I've found on google has not been helpful.
How do I create a class whitelist for user code in Java?
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I think that in your case you should create your custom class loader or use UrlClassLoader configured to load classes from specified URLs. Note that file in file system can be interpreted as URL to, so do not worry.
If for example you have 2 jar files foo.jar and bar.jar. foo.jar is permitted, bar.jar is restricted for the part of your application. Just add to the class loader's path the first jar only. The second will be invisible.
If you wish to throw SecurityException when forbidden classes are accessed yo have to implement your own class loader. It could be a composite of 2 URL class loaders: one with foo.jar, other with bar.jar in a classpath. The second class loader should override method loadClass and throw security exception every time the class is successfully loaded. Although I do not see serious benefits of this solution.