As it happens, I just saw this entry on how to remove a Root CA from the System Keychain:
http://radiotope.com/content/remove-certificate
Thanks,
Rich
I've used this to install new certs, part of the package deploys the new
certs to /tmp
Then this script picks them up and applies them.
If you need to delete, from the man page for /usr/bin/security
delete-certificate Delete a certificate from a keychain.
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#!/bin/bash
# post installation KeyChain secruity scripting for system Root
certificates
/usr/bin/security add-trusted-cert -d -r trustAsRoot -k
"/Library/Keychains/System.keychain" "/tmp/2011/foo.bar.com"
/usr/bin/security add-trusted-cert -d -r trustRoot -k
"/Library/Keychains/System.keychain" "/tmp/2011/IssuingCA"
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Hope this helps.