Hi! Thanks for your report. It seems to be an incompatibility with jekyll 3.1 and ruby-rouge 2.x. Installing an earlier version of ruby-rouge (like 1.9.1) makes pre tags appear again.
jekyll 3.2 is supposed to work fully with ruby-rouge 2.x and we are preparing an upload for it, which should then fix this bug. Cheers, Cédric
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