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When you generate an SSL certificate, you must include domain.com and www.domain.com – this is especially true with Let’s Encrypt / CertBot.
If you only specified domain.com when generating the SSL certificate, you’ll need to run it again and include both versions of the domain. This applies for all domains that you generate certificates for.
i.e. when passing -d, you’ll want:
-d domain.com -d www.domain.com
The only thing Let’s Encrypt / CertBot doesn’t support is WildCards, so you can’t pass:
-d *.domain.com
… at least not yet :-) (not sure if they plan to add this in the future).
When it comes to WildCards, the only way to truly support them without buying a specific certificate would be to manually hand-key all the domains and run them through the Let’s Encrypt / CertBot.
You can buy a WildCard SSL Certificate from NameCheap – they run $94-$99 / year. These types of certificates don’t have the same limitations, so you’d generate it once and it’d be valid for one domain, but any number of sub-domains.
i.e.
www.domain.com
my.domain.com
sub.domain.com
sub01.domain.com
etc.
The downside there is, of course, that you have to pay for the SSL Certificate each year. The upside, you don’t have to key in each sub-domain / sub-domain variation when you add a new one.
You could still use Let’s Encrypt / CertBot for domains that don’t need WildCards, but to truly support WildCards and not have to go through all the hassle, purchasing the certificate is the only way right now.