function run_atlantis

[ghost]

Currently being written to call in all of the load_atlantis_ncdf and other outputs to create the Rdata product which contains all truth. This function will load in numbers at stage, structN, resN, temperature, diet composition (proportions), diet biomass (using calc_pred_diet), call in model info (using load_meta), calculate length at stage (using calc_stage2length), and also catch inputs, for biomass and numbers -- see issue 'Fishing stage classes' since catch is currently only correct in total biomass per functional group per box, and not per age class.

• [x] finish and upload to Github
• [x] document
• [x] test that it plays nice with the other functions

[kellijohnson-NOAA]

Will need additional work later, but closing this issue as we need to work on other things and it has as much functionality as we currently need.