Add ITk pixel 3D radiation damage template correction + improvements in the setup

This MR adds the code needed to apply charge correction ot the ITk digitisation due to the radiation damage. The code has been tested on dummy (but realistic binning) histograms. Note that the changes do not affect the current code

The MR also updates the configuration a bit to make it easier/convenient to set some flags

cc @mbomben @kgrimm