Can't speak to most of the charges, but I can say that it is a documented fact that the clothing was intentionally insufficient.

What clothing that was made available was contracted to spec with the intention of it lasting only a limited time. The contracts called for clothing made on Union military apparel patterns, but with extremely sub-standard materials. The goal, apparently, was for the prisoner to have no clothes on his back by the time of his parole.

I don't personally have the documentation for this, but have seen it stated as documented fact in print.