Code:
for i in $(find ./ -name index.php); do cat $i |sed -e "s#<html>#<html><? include \(\"file\"\); ?>#" > $-new && mv $i-new $i;done
using the html as first line in the file
i know it can be done with first line crap :P awk,sed,vi you name it :D
too tired to think