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DNS can take up to 24 hours to update. Just because your registrar knows you changed your NS, doesn't mean everyone does. It takes a little while for everyone else to find out (generally because DNS servers have caches that need to expire).

CNAME setup should work on free CF accounts just fine. It must be done through cPanel though since it uses our nameservers instead of theirs. You won't even see mention of it on their website. I don't know much about it though since I use full zones myself (much more powerful and flexible if you don't mind the nameserver dance to add domains). To set up both domains on CF, you just treat them as if they weren't related. CF doesn't know they're on the same account or how they're added, and couldn't care less if it did. It just needs to know they're both hosted here. Set the addon domain to our servers and add it so it works (you've done this). Now go back to CF's website, and set up CF just like you did for the main domain. Create a zone for it, copy the DNS settings, then change the addon domain's name servers.

Yeah, I prefer the CF website too. Just figured I'd mention it since some users like it for the "CNAME Setup" it offers (which lets you have CloudFlare without messing with changing nameservers). The CNAME Setup option is completely incompatible with the CF website though, and in fact actually bars you from using the CF website if you pick it (it just says you must manage through cPanel).

Tommy seems to have crashed due to high load. The cause is still being investigated, but it likely has something to do with the lightning strike the other day. Marking solved since the server is working again.

You can create a new repository with a cron job, or if you say the name of the repo I can create it for you too.

Looks like tommy died a few hours ago (~3AM EDT). Escalating.