Revision 344111

Updated from Jakarta Commons IO 1.0 to 1.1. CopyUtils.copy() becomes IOUtils.copy() again. CopyUtils in 1.0 was not ideal design decision.
Fixed most of the unappropriate System.err/System.out/Exception.printStackTrace(). Those that aren't fixed and are not legitimate calls (in main() methods etc.) are marked with a TODO item.
Some Javadocs and style updates.