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I think it is an encoding issue of the new file
You can try this script:
def encoding = System.getProperty("file.encoding")
new File('fitnesse_tmp_result.xml').withReader(encoding) { reader ->
new File('fitnesse_result.xml').withWriter(encoding) { writer ->
def found = 0;
while ((line = reader.readLine()) != null) { if(line == "<?xml version=\"1.0\"?>" && ++found == 2) break writer.writeLine(line) }
}}
If it doesn't work, you can try to set directly the encoding variable to the real file endoding of fitnesse_tmp_result.xml, e.g. def encoding = "UTF-8"