This is my personal opinion, but I would prefer patches to be submitted relative to the project root. Looks like most patches have been, so no big deal there. However attachments of new files in JAR format are a pain. ZIP or TAR GZ files would be much easier to handle, with files relative to the project root.
JAR files /are/ ZIP files. They just use a different extension.
With annoying META-INF dirs.
--jason