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Your java code is a bit unusual. For a job like this I would usually use File.listFiles(FileFilter) and use the BufferedReader on each File in turn - I don't understand why you use a Process to do...

Put your code in a file by itself as the body of the main() method and *don't* try-catch exceptions - your main() method should be:

public static void main(String[] args) throws Exception

You...