Unknown args are now preserved if dieOnUnknownArg is false. Previously, they were ignored completely so wrapper scripts could not make use of them.
PHPCBF now has command line args to change its behaviour

--suffix=[suffix] will output a fixed version of each file with a filename suffix. Leaving this empty will overrite the file.

--no-patch will replace files with PHP instead of the patch command. This is useful if you are on a platform that doesn't support diff and patch.