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I have created an SSL certificate authority including a sub-authority to issue certificates. I have copied the root certificate to /usr/share/ca-certificates/extra and added it to /etc/ca-certificates, then ran dpkg-reconfigure ca-certificates and update-ca-certificates.

After it said "Adding debian:.pem done." I am now fairly convinced that Ubuntu knows about my CA.

Now I issued a certificate for the ZNC irc bouncer from the subca, installed it onto znc, but XChat will not trust the certificate despite all the above. I also issued a certificate to use with apache2 and that one works fine after adding the root ca to chromium. Does someone know how I can get XChat to trust the certificate?

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In case anyone is interested, the problem was that there were no execute privileges on /usr/share/ca-certificates/extras –  Silvio Sep 20 '12 at 17:52
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