I have a ruby script that makes iPhone App Store builds for me, but the zips it was generating wouldn’t get accepted by iTunes Connect. They were accepted if I used Finder’s “Compress” function.
millenomi’s answer came close for me, but this command is what ended up working. iTunes Connect accepted my build, and the app got approved and can be downloaded no problem, so it’s tested.
ditto -c -k --sequesterRsrc --keepParent AppName.app AppName.zip