The tool is described here
http://manual.calibre-ebook.com/cli/epub-fix.html (visible in Google) and is not listed here
http://manual.calibre-ebook.com/cli/cli-index.html and actually doesn't exist in current set of developer tools in Calibre for OsX.
It looks like a forgotten artifact, but doesn't makes me happier.
Is there any cli tool that can be used for generating opf manifests?