For me, military dwarves don't like to put away their cloths, but it's *nothing* like the kind of problem it was in 40d. In 31.x, the military dwarves' cloth-scattering habits are much closer to that of a civilian dwarf, aside from generating a few more objects (depending on how the military garb you have for them interacts with their civilian cloths). Especially once they reach the 'disable all Labors any time you blink' stage, and assuming they've got plenty of off-duty tiime, the military dwarves seem about as timely at putting clothing away as the rest of my forts. (earlier, while they still keep their civilian duties active, they don't tend to put cloths away much, since they have very little down-time: usually their either doing civilian jobs or individual training anytime they're not on active duty, leaving little opportunity for low-priority cloths pickup)
As far as making new cloths to replace the old rags, it would be important to note that non-uniform equipment won't actually get equipped. The dwarves may claim the new stuff, but they won't actually put it on - they'll keep a cabinet full of cloths while they run around naked, etc. The only way I've found to get the civilians to put on new clothing (after the old stuff has rotted away, or whatnot) is to draft them into their own military squads, assign them the 'civilian'-esque clothing I want them to wear, and simply never assigning them a training space (ie no barracks, armor rack, etc). You might need to station them somewhere once to get them to go pickup all their equipment, but overall, it's worked successfully for me, albeit a bit annoying to setup (initially) and with the new danger of accidentally sending out your squadron of legendary forgeworkers when you meant to send out your swordsdwarves ><.