It would be useful to include instructions on upgrading CertSage.php as new versions are released. Maybe upgrading isn't necessary since it seems most improvements are to make it easier for getting the first certificate and not renewals? But, since I don't know, I have upgraded. Just finally figured out how to do that with less work than starting from scratch. With my multiple subdomains and renamed main directory, it just means editing the certsage.php directory line again within the new copies put in each root directory. Maybe then run a "Test"?
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Sounds like you've got the gist of it. Most CertSage updates are for stability, performance, and/or ease of use. Rarely are there "breaking changes" that require generating a new CertSage data directory or the files within. Upgrading is usually a matter of downloading the new certsage.txt file, changing the data directory location line to point to the existing CertSage data directory (if needed), dropping the new certsage.txt into place, removing the old certsage.php, and renaming the new certsage.txt to certsage.php. The data files and cron job should not need to be modified. I deliberately make new CertSage versions as backwards compatible as possible and try to put warnings in the instructions when there are concerns with which to be aware. Of course, feedback such as yours is always helpful and appreciated to shape future updates. Update fatigue is certainly something on my mind and I will be keeping migration concerns in mind.
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I am running a WordPress multisite installation. All domains are managed by WordPress, all have /public_html as their root. No separate folders.
I'm able to successfully acquire and install certificates with certsage.php for my TLDs of which I have 3: example.com, example2.com, example3.com, all okay on one certificate. Thank you for that.
However, I am unable to do the same for the subdomains that are managed by WordPress: sub.example.com, etc.
I do have one subdomain not managed by WordPress and installed its certificate following your subdomain instructions.
Would creating a CertSage.sub.example.com directory and using a certsage_sub.php file with the directory path modified appropriately work? Other suggestions?
Thank you for your time and effort.
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From which directory is the content for the subdomain being served? You will need a copy of certsage.php in that directory that points to its own data directory for the corresponding certificate. You can copy your account keys over from your existing data directory to use the same ACME account.
Essentially, each webroot directory requires its own copy of certsage.php and therefore its own data directory.
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The content for the subdomains are dynamically routed by Wordpress Multisite from /public_html based on the requested subdomain.
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Are requests routed to retrieve content from specific, actual locations based upon the subdomain name or is the content dynamically served? In essence, can a certsage.php file be reached from a specific subdomain name?
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Dynamically served. If I browse to subdomain.example.com/certsage.php I get the certsage interface populated with my TLDs.
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Try creating a file named test (with no extension) that can be accessed via:
http://subdomain.example.com/.well-known/acme-challenge/test
If you can do that, I think there's a good chance. Please let me know.
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I get a 404 when I attempt that. However I can access it when I put it in the root folder. I can access it with my subdomain(s) and all 3 TLDs.
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The test file needs to be accessible from within /.well-known/acme-challenge/ in order to satisfy an HTTP-01 challenge.
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It appears that it is. What would the next step be?
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So long as CertSage can create challenge files for the subdomain names such that they are accessible alongside the test file, you should be able to acquire a certificate covering the subdomain names.
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Jonathan, I deleted my CertSage directory and started over. This time CertSage acquired the certificate for all TLDs and subdomains. I'm not sure what I did different, but pleased with the results. I did have to use cPanel to copy the certificates to the subdomains. Waiting to see what happens when the certificate expires.
Thanks so much for your help. 
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Glad CertSage worked for you! 
Keep an eye out and refining the process.
You can check out your certs being served with this tool:
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This may have been addressed elsewhere, but I can't find it.
I'm using CertSage for the first time. I downloaded the certsage.php file from GitHub and added it to the folder my domain serves from.
When I visit https://example.com/certsage.php, I see the page. However, in my folder, the certsage directory is not created, so I don't have a password to use.
Am I missing something?
Hosting on Namecheap shared hosting with cPanel 126.0 (build 27)
Running PHP 7.4
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The CertSage data folder is created one level higher than the folder your domain serves from. This is to keep its contents from being visible to the internet.
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Looks like the AI spam filter may have silenced you. I've inquired into that with the staff.
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Looks like you're unmuted now.
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Thank you for pointing that out. You were right, I was looking for the data folder in the project folder.
Got it to work & issued the certificates.
Thanks
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