The variable

can be used to pick if only retained catch is used, or all dead biomass is used. However, this functionality is only available within the extend_OM, and doesn't feed through so the user can pick it, so the default is just to use the retained catch.

Give users more options on what type of catch they are fitting. This is somewhat related to the discussion on #51 , as users can add in discards to the data frame coming from the MS, but it is not currently used by SSMSE: currently only catch or catch_F (which is really catch in terms of F) , are possible to be used by SSMSE, and either of these are assumed to be JUST retained catch.