[RFC] Preserve line-breaks and alignment in HTML docs.

I was trying to fix this - http://genometools.org/tools/gt_matchtool.html. Compare with this - http://yeban.github.io/genometools/www/genometools.org/htdocs/tools/gt_matchtool.html

I have tagged this RFC because ... I don't know if this is the right solution. I guess I could have worked on tools.conf asciidoc file but I wasn't sure it was worth the effort. I like how the html docs are formatted overall after this commit, but I am not able to decide if this commit does justice to say http://yeban.github.io/genometools/www/genometools.org/htdocs/tools/gt_gff3.html. See how lines are now split compared to http://genometools.org/tools/gt_gff3.html.