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
Since we always compare this to chars, would it make sense to just make it a char? I think you can write `char UTF8_BOM_CODE = '\uFEFF'` (or actually `char BOM = '\uFEFF'` since that character is the byte order marker regardless of which encoding you use). Then you don't have to cast at line 1214.