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This links the SOS logo to the official master-branch location and changes the version badge to use img.shields.io, which appears to be less finicky than badge.fury.io.
Side note: the landing page for the Travis badge (which defaults to the latest PR, not the latest master build) appears to be a "won't fix" issue that's been closed years ago:
travis-ci/travis-ci#655
certbot/certbot#927
I think our valid options are to 1) leave it as is, 2) remove it, 3) link to the "branches" page, or 4) link to the "builds" page. I don't see any way to link to the latest master build...