Mobs' armor, weapons, and whatnot are considered "rare drops" and will only drop if the mob is killed by a player. Protip, potions thrown by players also count as player kills, so if your automation can get the skellies down to 1 HP, you can throw an instant health potion to kill them all at once.59 apparently
also, does anyone know if the skeletons will need to be killed by hand for them to drop the equipment they spawned with? (spawned from a roguelike dungeon spawner) or can I use a simple piston to kill them and get the stuff?
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Also note that there are several mod blocks that can emulate player kills, ranging from ExtraUtils spikes to the MFR Grinder to some Thaumcraft golems. These are the same things that will give XP when they kill a mob, so if you're not sure where to look, that's a good place to start.
But no, your piston won't do it, unless you punch the skellies within a few seconds of their suffocation.