Manually deleting the Safari cookies on Yosemite is not working

Solution 1:

I don't understand the full interplay, but rebooting will fix cookie retention [presumably held in cache] - that is separate from login details remembered by Keychain & also Form Values etc.

If you really want a clean sweep, try OnyX (free/donationware) > Cleaning > Internet - choose what you need to delete from there…

Safari has its own simpler version, though I'm not certain quite what it does delete…

Solution 2:

Not sure if I fully understand your question, but if you are looking for a way to remove all cookies from Safari via the terminal, without having them regenerated the next time you launch Safari: try the shell script posted below. (I copied this answer from my original post here: https://apple.stackexchange.com/a/273442/201104.)

I tested this on macOS 10.12.3 and Safari 10.0.3 and it works.

Warning: The tests I did weren't as thorough, meaning: some of the files deleted by this script might not actually be necessary in order to achieve the removal of the cookies, you should trial-and-error your way around it to narrow it down if you like. I personally use the script 'as is', but in your personal situation that might mean you'll lose some data that you actually wanted to keep.

Copy this into a simple shell script and run it (be sure to also copy the 'killall' command):

rm -rf ~/Library/Safari/History*
rm -rf ~/Library/Safari/Auto*
rm -rf ~/Library/Safari/LocalStorage
rm -rf ~/Library/Safari/Downloads.*
rm -rf ~/Library/Safari/Databases
rm -rf ~/Library/Safari/SearchDescriptions.plist
rm -rf ~/Library/Safari/WebFeedSources.plist
rm -rf ~/Library/Safari/Last*
rm -rf ~/Library/Safari/Recently*
rm -rf ~/Library/WebKit/com.apple.Safari
rm -rf /Library/Cookies
rm -rf ~/Library/Cookies
rm -rf ~/Library/Caches
rm -rf /Library/Caches
rm -rf ~/Library/Application Support/Oracle/Java/Deployment/cache
rm -rf ~/Library/Preferences/Macromedia/*
rm -rf ~/Library/Containers/com.apple.Safari.*
rm -rf ~/Library/Application Support/com.apple.sharedfilelist/*
rm -rf ~/Library/Preferences/com.apple.coreservices.useractivityd.dynamicuseractivites
rm -rf ~/Library/Preferences/*SpotlightNetHelper*
rm -rf ~/.oracle_jre_usage
rm -rf ~/Library/Preferences/com.apple.sharekit.recents.plist
rm -rf ~/Library/Saved*

killall -KILL nsurlstoraged