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sorry "MSFarmerSpriteCustomizer_1_0_0" there are layers for all the clothing pieces but I dont see any layers for the weapons to go on, do these need to be introduced in some way?? I don't see weapons within the program at all

Ah, that explains the confusion. This isn't the Farmer Sprite System that you're commenting on. This is a different asset.

To answer your questions, the Sprite Customizer just creates a flattened version of the layered clothing sheets, with custom colors. This is useful for devs who are not making a paper doll system. You still need to create the animations in your game engine. Consult the included animation guide for help with that.