Quote:
clean the code generated by Atlantis, for instance:
<h3 class="h31" id="ncx3">Internal</h3>
becomes:
<h3 id="ncx3">Internal</h3>
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I do not think that what you are doing can be called "cleaning". If you have "h3" elements associated with different CSS classes, there are differently formatted "Heading 3" paragraphs in your source document. You are not "cleaning the code". You are removing formatting present in the source document.