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Middleman[1] and a rake task running rsync.

Nice, middleman is a well designed SSG :) Are these all your personal sites, or do you maintain websites for customers?

Just mine

Do you have a VPS where you host them? Why not use Github Pages?

I use EC2 + letsencrypt with custom domain. Last time I checked github did not support SSL for custom domains.

Cloudfront is not end to end encryption.