In a structure like a limb different pattern generating methodologies will be acting at the same time. Collagen fibres in the extracellular matrix will be assembling because of the shape of tropocollagen molecules, protein will be forming on RNA templates and RNA will be forming on DNA templates in every cell. Mesoderm and ectoderm will be interacting to form non-copy template patterns. The pattern forming properties might be intrinsic, or extrinsic. We can simplify matters a little by sticking with our limb.
Limbs have a limited number of tissue types.
We can rule out the circulatory system because that develops late, after the patterns have been established. The skin and its precursor the ectoderm is not responsible. The ectoderm, of course, interacts with the mesoderm to produce the outgrowth of the limb, but transplanting ectoderm from forelimb to hindlimb still leaves a hindlimb, and vice versa. So it looks as if the pattern lies in the skeleton or the muscles. We don't really know, but at least we are narrowing the field.