Here is the command I have used successfully:
zip -Xr epubfilename.ePUB mimetype META-INF OEBPS -x \*.DS_Store
This places files in the right order (mime type first, then META-INF with container.xml next, finally everything else) and excludes .DS_store since it looks like you are on a Mac.
Note that you will need to do this from within the book.epub.d directory in your example to produce the correct output.
I also recommend double checking results with epubcheck (https://github.com/IDPF/epubcheck or http://validator.idpf.org) if you are not already doing so.