Zips would support including external attributes like the executable bit of files - this currently isn't done, so when a zipfile of a folder is downloaded, shell scripts stop being executable after unzipping
See https://pkware.cachefly.net/webdocs/casestudies/APPNOTE.TXT sections 4.3.12 & 4.4.15 as well as http://www.forensicswiki.org/wiki/Zip#External_file_attributes