ReshapeMatFiles is currently used only for posterior IRF's. For large models it is a huge bottle-neck which is probably useless. The approach followed in prior_posterior_statistics.m is to use the pm3 utility that takes the data needed for plots from the non-reshaped files. Such a procedure is in the end much less time consuming than the ReshapeMatFile.
The current pm3 utility is not easily extended for irfs (matrices are 4-dimensional for irf's). However I tried to write a pm4 utility for 4-D matrices which looks interesting.
How about removing the call in posteriorIRF to: ReshapeMatFile posteriorIRF_core2 (the plot utility for bayesian irf's which uses the reshaped files)
add making a new call to a pm4.m utility that replicates the behaviour of pm3 to 4-D matrices?