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
Please add a check to insure this only occurs at the beginning of the the file.