Moved output dir creation to output phase.

    # Call this after input parameters set

    def run

      clear_dir(@output_dir)

      if @export

        FileUtils.mkdir(@output_dir)

        init_output_dirs(@output_dir)

      else

        copy_template(@template_dir, @output_dir)

      end

      parsed_files = @timer.time(:parsing) { parallel_parse(@input_files) }

      result = @timer.time(:aggregating) { aggregate(parsed_files) }

      relations = @timer.time(:aggregating) { filter_classes(result) }

      warn_globals(relations)

      warn_unnamed(relations)

      clear_dir(@output_dir)

      if @export == :json

        FileUtils.mkdir(@output_dir)

        init_output_dirs(@output_dir)

        @timer.time(:generating) { write_src(@output_dir+"/source", parsed_files) }

        @timer.time(:generating) { write_json(@output_dir+"/output", relations) }

      else

        copy_template(@template_dir, @output_dir)

        @timer.time(:generating) { write_src(@output_dir+"/source", parsed_files) }

        @timer.time(:generating) { write_tree(@output_dir+"/output/tree.js", relations) }

        @timer.time(:generating) { write_members(@output_dir+"/output/members.js", relations) }