Separate running of OM and EM in ss3sim_base() into separate functions

[kellijohnson-NOAA]

Another idea @latreesedenson-NOAA and I thought of yesterday related to this one is separating the OM modifications, sampling, and EM running in ss3sim_base into separate functions so that they can be called independently by users if need be.

For instance, @latreesedenson-NOAA needs to add in some environmental data before running the EM, so it would be helpful to first just get the om and sample, then run custom code to add in the environmental data, and finally run the EM (with bias adjustment).

Originally posted by @k-doering-NOAA in #300 (comment)