Basically, you need to replace the Google Analytics at the bottom of
page-structure.xsl with this structure:

  <xsl:choose>
    <xsl:when
 
test="substring-after(/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='request
 '][@qualifier='URI'], 'handle/123456789/')='123'">
      <!-- GA javascript with ID for collection 123 goes here -->
    </xsl:when>
    <!-- repeat xsl:when for other collections -->
    <xsl:otherwise>
      <!-- GA javascript with ID for every other collection goes here -->
    </xsl:otherwise>
  </xsl:choose>

By rewriting this code, ignore what's in dspace.cfg and embed your GA
IDs directly into the javascript snippets.

Regards,
~~helix84

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