Fix command line tool to take one file
Fix command line tool to take one file

* -infile file and outputs to -outdir specified directory
or defaults to /tmp/geodesyml/runall
* If run with no arguments it by default specifies the -indir
as src/test/resources/sitelog and outputs by default to
src/test/resources/sitelogtoGeodesyML


Former-commit-id: 51d9dace7aa7f3459d0741df0e97337181128968
GeoscienceAustralia/Geodesy-Web-Services,GeoscienceAustralia/geodesy-domain-model,GeoscienceAustralia/Geodesy-Web-Services,GeoscienceAustralia/Geodesy-Web-Services,GeoscienceAustralia/Geodesy-Web-Services,GeoscienceAustralia/geodesy-domain-model