dehydrated uses the file domains.txt as configuration for which certificates should be requested.
The file should have the following format:
example.com www.example.com
example.net www.example.net wiki.example.net
example.net www.example.net wiki.example.net > certalias
This states that there should be two certificates example.com and example.net,
with the other domains in the corresponding line being their alternative names.
You can define an alias for your certificate which will (instead of the primary domain) be used as directory name under your certdir and for a per-certificate lookup. This allows multiple certificates with identical sets of domains but different configuration to exist.
Certificates with a wildcard domain as first (or only) name require an alias to be set.
Aliases can't start with *..