I would really appreciate it if you would add a config option to your mod. A simpel option that the last item of a stack get not used up on crafting.

At the moment its quite difficult to keep items stocked and shift clicking while crafting removes whole stacks so that filling pipes (EnderIO or so) may put other items in the slots.

Another possibility to improve this, could be a gui or wrench setup where you can specify how many stacks a ingredient can use.

edit: be aware that there are items from HarvestCraft that get not used up on crafting and that have a stack size of one ;).