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I use kramdown with Rouge in my Jekyll site.
I notice that kramdown compiles inline code to <code class="highlighter-rouge">inline code</code> instead of simply <code>...</code>. While it would be nice to be able to turn off highlighting in inline code, no biggy.
When I set line_numbers: true, however, things get ugly: Rouge can or does not distinguish between inline and block code, and translates the inline code into a block with line numbers -- clearly not as intended!
(The created code looks broken beyond that, too.)