To unzip the epub, move the ePub to a folder, cd to it then simply:

unzip MyEbook.epub

To zip up an epub:

1. zip -X MyNewEbook.epub mimetype

2. zip -rg MyNewEbook.epub META-INF -x \*.DS_Store

3. zip -rg MyNewEbook.epub OEBPS -x \*.DS_Store

Some explanations necessary here. We start each line with two flags:

-r (recursive)

This means move down through any directories/folders recursively, ensuring that everything in the folders specified gets included

-g (grow file)

even more concise :
      

// To unzip the epub, move the ePub to a folder, cd to it then simply:

zip -rX ../my.epub mimetype META-INF/ OEBPS/

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Without -X you could get the following when validating it with EpubCheck:

ERROR: my.epub: Mimetype entry must not have an extra field in its ZIP header

If mimetype is not the first in the epub file EpubCheck prints the following:

ERROR: my.epub: Mimetype entry missing or not the first in archive

Linux uses the name of the current folder as the epub filename:
zip -rX "../$(basename "$(realpath .)").epub" mimetype $(ls|xargs echo|sed 's/mimetype//g')

I found this version also worked better for epubs I found that don't use the OEBPS folder. I don't know if not having that folder is valid per standards, but I found examples of it being missing in the wild.