I've found a solution that I like (and doesn't involve complicating pandoc).

    pip install htmlmin
    echo -e 
'<div><pre><code>hello</code></pre><pre><code>world</code></pre></div>' | 
pandoc -t html5 | htmlmin -s

To answer your question:

We write markdown by hand, which contains code blocks full of custom 
elements (for highlighting).  Our custom format is <r:b>bold</r:b> within 
the codeblock.  Using a pandoc filter, those custom blocks get turned into 
this HTML:

    <pre class="bold"><code>bold</code></pre>

We then use http://www.princexml.com/ to convert from HTML to a PDF.

Thanks!

On Friday, April 8, 2016 at 10:35:10 AM UTC-6, Matthew Pickering wrote:
>
> Can you please describe what you are doing? You mention that you're 
> going markdown -> html -> pdf (why?) 
>
> The answer to your question is that pre is a block level element and 
> pandoc inserts newlines after each block from what I remember. 
>
> On Fri, Apr 8, 2016 at 5:24 PM, Matt Haggard <hagg...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org 
> <javascript:>> wrote: 
> > Bah... google groups messed up the newlines, but maybe you get the idea? 
> > 
> > On Friday, April 8, 2016 at 10:23:55 AM UTC-6, Matt Haggard wrote: 
> >> 
> >> I have a filter that adds elements to code blocks (for bolding, 
> italics, 
> >> etc.).  We go markdown -> html -> pdf and have noticed that sometimes 
> there 
> >> is an extra erroneous space between these custom elements in the final 
> PDF. 
> >> This breaks copying and pasting. 
> >> 
> >> It's because pandoc adds newlines between some elements in the 
> generated 
> >> HTML.  This shows and example: 
> >> 
> >> echo -e 
> >> '<div><pre><code>hello</code></pre><pre><code>world</code></pre></div>' 
> | 
> >> pandoc -t html5 
> >> 
> >> <div> 
> >> 
> >> <pre><code>hello</code></pre> 
> >> 
> >> <pre><code>world</code></pre> 
> >> 
> >> </div> 
> >> 
> >> 
> >> Is there a way I can get the output of the above to instead be this? 
>  (or 
> >> even match the original input string) 
> >> 
> >> echo -e 
> >> '<div><pre><code>hello</code></pre><pre><code>world</code></pre></div>' 
> | 
> >> pandoc -t html5 
> >> 
> >> <div> 
> >> 
> >> <pre><code>hello</code></pre><pre><code>world</code></pre> 
> >> 
> >> </div> 
> >> 
> >> 
> >> Thank you! 
> > 
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