Imported a subset of apache commons fileupload into sparkle. Then imported a portion of apache commons io, which fileupload depended on. Altered the InputFilesPhaseListener to use the imported code, and removed the old jar and any ant usage of the jar.
It took a certain amount of effort to limit the io dependencies, as each class pulled in more and more of it. Finally, I found a way to include all of upload, even the parts we don't currently use, while truncating the io that we pulled in.