JAL-4420 Allow preprocessing of arguments if they are all simply filenames (or URLs...

JAL-4420 Allow preprocessing of arguments if they are all simply filenames (or URLs).  Preprocessing involves adding --open arguments, and spotting and regrouping associated files such as annotations, features and tree files.  These get --annotations argument etc.  Add FileUtils tools to get basepath and extension of filename or URL whilst only in String form.