In Automator create new workflow with the following settings
Service recieves selected: files or folders
in: Finder.app
Run Shell Script
Shell: /bin/bash
Pass input: to stdin
while read -r p; do
zip -d "$p" "__MACOSX/*" || true
zip -d "$p" "*.DS_Store" || true
zip -d "$p" "*.git/*" || true
zip -d "$p" "*.gitignore" || true
zip -d "$p" "*.sass-cache/*" || true
zip -d "$p" "*.codekit-cache/*" || true
zip -d "$p" "*.codekit" || true
zip -d "$p" "*.codekit3" || true
done
while read -r p; do
zip -d "$p" __MACOSX/\* || true
zip -d "$p" \*/.DS_Store || true
zip -d "$p" \*/.git/\* || true
zip -d "$p" \*/prepros.config || true
zip -d "$p" \*/_Changelog.html || true
zip -d "$p" \*/_Description.html || true
zip -d "$p" \*/_Features.html || true
zip -d "$p" \*/_Upcoming.html || true
done
Then save this as service with the name Clean Zip.
To clean any zip file, right click on it, go to services -> Clean Zip.