I have created a certificate with the certonly and --standalone tags and multiple domains with -d domain.com -d extra.domain.com etc. However, the certificate subject is not the first domain I listed, but one of the subdomains. So instead of domain.com, the certificate is issued to extra.domain.com, is there some setting where I can change the subject of the certificate?
Take a look at this reply for more background on this issue and possible solutions:
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Hello @qmaster312,
Take a look to this @pfg post, it is a bug introduced in letsencrypt-auto client 0.5.0:
In that post you have 3 solutions 
Edit: @pfg was a few seconds faster than me 
Cheers,
sahsanu
Thank you, I guess i’ll just wait for 0.6.0.
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