namespace required in transform

I've created a transform that takes an xml file, not knowing what is in it, just resolves any references between documents or within document, and results in one big xml file, with all relevant information contained.

My problem is it seems I have to declare all the namespaces in my first xml document, in the transform file as well.  I get "Exception:  System.Xml.Xsl.XsltException: Prefix 'whatevernamespace' is not defined." 
This goes away if I add the namespace to the transform.  However, I am going to be dealing with multiple xml files, and I won't be able to know in advance what all the namespaces are.  How can I handle this?

Thank you,
Karen
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