Make use of r4ss::run() and other functions for moving files and running models?

[iantaylor-NOAA]

The r4ss issue https://github.com/r4ss/r4ss/issues/460 "create a single function for running SS models for use in r4ss, SSMSE, and ss3sim" has been resolved thanks to PR https://github.com/r4ss/r4ss/pull/722 so the modified functions are available for use in SSMSE. I'm not sure it's worth making changes here if the status-quo functions are working, but future developments could consider moving to the new r4ss functions.

Note this is a repeat of https://github.com/ss3sim/ss3sim/issues/385.