Well XSLT has the document function
http://www.w3.org/TR/xslt#document to deal with multiple input documents for a single transformation.
On the other hand you seem to want to transform HTML documents and not XML documents so you need to make sure you use a HTML parser in your tool chain that is able to parse HTML and pass the result on to the XSLT processor. With Java you can use TagSoup and Saxon to do that, Saxon has an option to allow that:
http://www.saxonica.com/documentatio...mand-line.html
Microsoft MVP - XML