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The meshes/stl files provide just the (rigid body) link geometry for a link of your robot and nothing more. Where a STL shows up of course depends on where the origin (i.e. 0/0/0 coords/axes) is located in the STL and where it is placed in the URDF using the <origin>
element. The rotation axes are defined using the <axis>
element inside a <joint>
.