RemoveBOM.java

import java.io.*;
import java.nio.charset.StandardCharsets;

public class RemoveBOM {

  public static void main(String[] args) {
    File directory = new File(args[0]);
    removeBOM(directory);
  }

  private static void removeBOM(File file) {
    if (file.isDirectory()) {
      File[] files = file.listFiles();
      if (files != null) {
        for (File f : files) {
          removeBOM(f);
        }
      }
    } else if (file.getName().endsWith(".java")) {
      try (FileInputStream fis = new FileInputStream(file);
           InputStreamReader isr = new InputStreamReader(fis, StandardCharsets.UTF_8)) {
        int bom = isr.read();
        if (bom != '\ufeff') {
          return;
        }
        try (FileOutputStream fos = new FileOutputStream(file);
             OutputStreamWriter osw = new OutputStreamWriter(fos, StandardCharsets.UTF_8)) {
          osw.write(bom);
          int c;
          while ((c = isr.read()) != -1) {
            osw.write(c);
          }
        }
      } catch (IOException e) {
        e.printStackTrace();
      }
    }
  }
}