FIX/Include run number in out -folder path if missing

@karnem with your last additions for removing the run from the folder as it is always written in the webservice. The pdfs are stored outside of the folder if calibration is ran through the command line

xfel_calibrate/calibrate.py

@@ -791,6 +791,12 @@ def run():
                                         caltype.upper(), datetime.now().isoformat())
         if try_report_to_output:
             if "out_folder" in args:
+                if "run" in args and str(args["run"]) not in args["out_folder"]:
+                    rr = args["run"]
+                    # Only put run, when it is not in the out_folder
+                    if isinstance(rr, int):
+                        rr = "r{:04d}".format(rr)
+                    args["out_folder"] = "{}/{}/".format(args["out_folder"], rr)
                 out_path = os.path.abspath(args["out_folder"])
             else:
                 print("No 'out_folder' defined as argument, outputting to '{}' instead.".format(