Looking into this a bit more, I think the openssl x509 "-addtrust" and "-setalias" commands are the ones I want, but if I try and set these after the cert has been signed then the cert can't be imported.
Is there any option to set these values in OpenCA at cert signing time ?
No, there is no option to do this today but I checked the code because of the import problems. It looks like OpenCA::X509 is the major problem. It uses the following string:
$self->{beginCert} = "-----BEGIN CERTIFICATE-----";
Perhaps you have to verify where it is used and change it a little bit. Perhaps it is enough to change beginCert and endCert by replacing the blank by \s+(|.*\s+).
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