If you unpack a xpi file with med-xpi-unpack, it will also unpack jar files. med-xpi-pack will later pack those unpacked jar files, before adding them to xpi file.
If you already have easy unpacked xpi file, the new med-xpi-pack will add the jar files to xpi file, but won't remove them afterwards, so I think that will fix this bug.
I don't think you will need to rebuild a package.
If you unpack a xpi file with med-xpi-unpack, it will also unpack jar files. med-xpi-pack will later pack those unpacked jar files, before adding them to xpi file.
If you already have easy unpacked xpi file, the new med-xpi-pack will add the jar files to xpi file, but won't remove them afterwards, so I think that will fix this bug.