Redundant/commented out code

[DrPaulSharp]

The use of the following routines in the code is not clear (calls to them are either commented out or not present). I need a hand working out what they are used for. If they are not required, they should be deleted.

compile/reflectivityCalculation/reflectivityCalculationCodeOnlyScript.m -- is required
compile/reflectivityCalculation/setCompilePaths.m - Removed in #255

minimisers/DE/runDE.m - function "PlotIt" - Removed in #178

minimisers/DREAM/lowerCaseStruct.m - Removed in #357
minimisers/DREAM/mvnorpf.m
minimisers/DREAM/Diagnostics/chisRnd.m
minimisers/DREAM/functions/DREAM.m - has this been replaced by ratDREAM.m?
minimisers/DREAM/functions/evaluateRATModel.m - Removed in #178
minimisers/DREAM/functions/GL.m
minimisers/DREAM/functions/initializeDREAMForRAT.m - Removed in #178
minimisers/DREAM/functions/measError.m
minimisers/DREAM/functions/setupDREAMForRAT.m - Removed in #178
minimisers/DREAM/functions/whittle.m
minimisers/DREAM/postprocessing/DREAMPostprocessing.m
minimisers/DREAM/postprocessing/genParSet.m
minimisers/DREAM/postprocessing/predMCMC.m

minimisers/generalUtils/checkBounds.m - Removed in #357
minimisers/generalUtils/bayesStats/calcMCMCstatRefErrors.m - Removed in #357
minimisers/generalUtils/bayesStats/confIntervals.m - Removed in #357
minimisers/generalUtils/bayesStats/packPriors.m - Removed in #356
minimisers/generalUtils/bayesStats/ratInputs.mat - Removed in #357
minimisers/generalUtils/bayesStats/ratTest.m - Removed in #357

minimisers/NSMain/loopCell.m - Removed in #357
minimisers/NSMain/parseBayesResults.m - Removed in #357
minimisers/NSMain/plotLivePointsWithEllipses.m -- Removed in #264

targetFunctions/common/groupLayers/allocateLayersForDomainsContrast.m - Removed in #264
targetFunctions/common/reflectivityCalculations/abeles/orso_test0.m - Removed in #178
targetFunctions/common/reflectivityCalculations/abeles/orso_test1.m - Removed in #178
targetFunctions/common/reflectivityCalculations/abeles/orso_test7.m - Removed in #178
targetFunctions/common/reflectivityCalculations/abeles/test0.dat - Removed in #178
targetFunctions/common/reflectivityCalculations/abeles/test1.dat - Removed in #178
targetFunctions/common/reflectivityCalculations/abeles/test7.dat - Removed in #178

utilities/misc/kde.m

Whilst looking through these files, I am also concerned about function calls where the number/order of arguments does not appear to match the argument list in the routine.
Also, why is customModelClass a class? -- it has no properties, and only static methods. -- This is changed in #178