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OK...
So letsencrypt have a rate limit on the number of certs [INCLUDING SUB DOMAINS] you can create/renew per week.

So if you have a lot of sub domains and not "one cert for all" : good luck you are f.ed.

@dashie There's a support for wildcard certs planned for 2018, until then, you have only this :/

@dashie Personally my workaround consist in making "buckets" of certs for differents things, like one for "public" subdomains and one for "private" subdomains

@KokaKiwi yeah I think I will have to revert to that...
and anyway, no certs are private, crt.sh are indexing all...

KokaKiwi @KokaKiwi

@dashie Yeah by "private" I mean the ones I don't want them linked to "public" domains and then allowing to simply look the SAN entry for one "public" domain to find the "private" ones

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@KokaKiwi even if only "public" ones are listed in master in the certs, the SANs are visible so well, it's juste "not easier" to find them, nothing more

@dashie No I mean I have two separate certs, one with SANs with "public" domains, and one with SANs with only "private" domains, I'm testing searching them in crt.sh but I can't manage to find them easily so well...

@KokaKiwi I have all my sub domains even "privates" one under the same domain so well, it's a fail anyway.