Stripped BOM from UTF 8 encoded files

The compiler throws an exception when a flag file or a conformance configuration file has a UTF-8 BOM, so stripping it in both of these cases would be beneficial for people that use Visual Studio, or other IDEs that add a BOM by default.
Fixed https://github.com/google/closure-compiler/issues/658
I think this should be:

if (isFirstCharacter) {
  isFirstCharacter = false;
  if (c == UTF8_BOM_CODE) {
    continue;
  }
}