In your customization stylesheet, override the "chunk" template (found in html/chunk-common.xsl) and change the logic for what constitutes a chunk. For instance, to say that sections are not chunks, change it to this:

<xsl:template name="chunk"> <xsl:param name="node" select="."/> <!-- returns 1 if $node is a chunk -->

<xsl:choose> <!-- comment out these lines to make sections not be chunks <xsl:when test="name($node)='sect1' and count($node/preceding-sibling::sect1) > 0">1</xsl:when> <xsl:when test="name($node)='section' and count($node/parent::section) = 0 and count($node/preceding-sibling::section) > 0">1</xsl:when> --> <xsl:when test="name($node)='preface'">1</xsl:when> <xsl:when test="name($node)='chapter'">1</xsl:when> <xsl:when test="name($node)='appendix'">1</xsl:when> <xsl:when test="name($node)='article'">1</xsl:when> <xsl:when test="name($node)='part'">1</xsl:when> <xsl:when test="name($node)='reference'">1</xsl:when> <xsl:when test="name($node)='refentry'">1</xsl:when> <xsl:when test="name($node)='index' and (name($node/parent::*) = 'article' or name($node/parent::*) = 'book')">1</xsl:when> <xsl:when test="name($node)='bibliography' and (name($node/parent::*) = 'article' or name($node/parent::*) = 'book')">1</xsl:when> <xsl:when test="name($node)='glossary' and (name($node/parent::*) = 'article' or name($node/parent::*) = 'book')">1</xsl:when> <xsl:when test="name($node)='colophon'">1</xsl:when> <xsl:when test="name($node)='book'">1</xsl:when> <xsl:when test="name($node)='set'">1</xsl:when> <xsl:when test="name($node)='setindex'">1</xsl:when> <xsl:otherwise>0</xsl:otherwise> </xsl:choose> </xsl:template>

Hope this helps.

-M