I'm sure there is a better solution, so I'm going to leave this open.
However, my solution was to refactor all the package names to add one folder to the base.
e.g. org.apache.commons.fileupload.FileUpload
Becomes: include.org.apache.commons.fileupload.FileUpload
Since my name is unique, nothing else should use it and my code won't use anything else.
Since its just one folder deeper, I can swap out newer versions of the Apache Commons FileUpload simply by throwing the source within the "include" directory.
If no one else has a solution, hopefully this will help someone else out.