I have succeeded producing an epub3 following the README but I have change the command :
xsltproc --stringparam base.dir ebook1/OEBPS/ epub3/chunk.xsl mybook.xml
xsltproc --stringparam base.dir ebook1/EPUB/ epub3/chunk.xsl mybook.xml
with these options I get
<rootfile full-path="OEBPS/package.opf" ....>
I have got another problem mimetype and MMETA-INF are stored in a file called EPUB..
toc and .opf files are also prefixed with EPUB (or OEBPS) if I use the standard command line.
Thanks for your work