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Since PDF output is primarily obtained by running XSLT transformations over the DITA input files, one customization method would be to override the default XSLT templates that are used by the PDF transformation.

The pdf-css-html5 transformation type uses two stages to transform the merged DITA map (the one that aggregates all the topics) to HTML5:
  1. Stage 1: Makes some changes on the merged map and the result is a modified merged map. This stage can be altered by implementing the com.oxygenxml.pdf.css.xsl.merged2merged XSLT extension point. This extension overrides the stylesheets found in the following folder: DITA-OT-DIR\plugins\com.oxygenxml.pdf.css\xsl\merged2merged.
    Note: Use this when you need to filter DITA content.
  2. Stage 2: Transforms the merged map to HTML5 and the result is a single HTML document. This stage can be altered by implementing the com.oxygenxml.pdf.css.xsl.merged2html5 XSLT extension point. This extension overrides the stylesheets found in the following folder: DITA-OT-DIR\plugins\com.oxygenxml.pdf.css\xsl\merged2html5.
    Note: Use this when you need to change the HTML structures generated for a specific DITA element.

These extension points can be used either from a Publishing Template or a DITA-OT extension plugin.