update readme

Author: jtmims

tools/run-MDTF/README.md

@@ -2,5 +2,7 @@
 MDTF shell driver to assist model development at the GFDL <br />
 Command-line usage:
 ```
-run-mdtf.sh /path/to/pp/dir/pp out_dir/mdtf startyr endyr
+run-mdtf.sh -i /path/to/pp/dir/pp -o out_dir/mdtf -s startyr -e endyr
 ```
+This script requires a user inputted `pod_config.json`. One is supplied by default, but may need to be updated in order to launch more PODs or update realm information!
+A new one can be supplied with the `-l` OPTARG.