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I believe you're right—this is some shell variable issue on my box, and has nothing to do with certs or calibre. Sorry for the misdirect.
For some reason, sudo commands aren't being passed the http_proxy and https_proxy environment variables. These are set in the user space, and I've made sure that they're both set in the user and root's ~/.profile, yet sudo commands don't get these variables. It will take some more digging—I haven't seen behavior this before.
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