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java unicode conversion on linux not working on max os x

Chances are you'tr not reading the file correctly to start with. You haven't shown how you're reading the file, but my guess is that you're just using FileReader, or an InputStreamReader without specifying the encoding. In that case, the default platform encoding is used - and if that's not the actual encoding of the file, you won't be reading the right characters. You should be able to detect that without doing any replacement at all.

Instead, you should use a FileInputStream and wrap it in an InputStreamReader with the correct encoding - which is likely to be UTF-8 as it's XML. (You should be able to check this easily.)

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