At the top of xhtml/docbook.xsl and html/docbook.xsl
you can find:
<xsl:output method="xml" encoding="UTF-8" indent="no"
doctype-public="-//W3C//DTD XHTML 1.0 Transitional//EN"
which seems to overwrite the indent and doctype-*
settings of the user. IMHO they should be removed
there, so the user decides and chunker.* takes precedence.
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