This function reads in all of the information contained in the admodel.hes file. Some of this is needed for relaxing the covariance matrix, and others just need to be recorded and rewritten to file so ADMB "sees" what it's expecting.
Directory in which .hes file is located.
Name of .hes file.
A list with elements num.pars, hes, hybrid_bounded_flag, and scale.
Explanation of the methods (in PDF form) published here: https://github.com/admb-project/admb-examples/blob/master/admb-tricks/covariance-calculations/ADMB_Covariance_Calculations.pdf
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