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dayvidwhy

In your position I did these things; - Removed the CNAME record; - Changed my A records to point to githubs https ip's - Deleted the site from cloudflare - Purged my cache for the site in chrome (chrome appears to remember who your site has its cert with for a bit?) - Profit
yeah you could setup the github ssl as per their instructions, then put cloudflare in front of it. See their options here https://support.cloudflare.com/hc/en-us/articles/200170416-W...

I was previously using the partial ssl option and am quite happy that I don't have to continue with this pseudo ssl that has an unsecure link.