After many hours of banging my head against the keyboard I finally have custom syntax highlighting with ckeditor in Drupal 6. When I first set out to add this feature I thought it would be as easy as trun a module on and your good to go. Turns out that isn't the case. I originally tried to use GeSHi with the wysiwyg module and the ckeditor javascript library. I got subpar results with this method.
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