Fixed an error in the calculation of flux uncertainties for the output arrays. Covariances are now only calculated for TC regions (23,23) and not for the full state vector.

Had to replace a few lines to ensure proper writing of prior fluxes to the files. Until now, prior fluxes 
were retrieved from a savestate.nc file (and erroneously, the poterior was read by default) while the "old"
method to provide priors was as unscaled fluxes (all multipliers equal to 1.0). This behavior is now back.

routine can now be run as part of a cycle so that analysis finishes directly instead of post-processing

TransCom files are now created based on a 1x1 to TC conversion, note that there is no covaraince yet