just delete all <root>,</root> and <?xml...> after the second line and add a </root> at the end.

perl -pi.bak -e 'next unless $. > 2; s{</?root>\s*}{}; s{<\?xml.*\?>\s
+*}{};' foo.xml
echo '</root>' >> foo.xml
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can't quite figure out how to leave that last </root> alone or how to add it at the end of processing...