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The EAGLE docs says the Reference layer (#49) is for "reference marks".

Is this referring to mechanical data for automated assembly such as fiducials and component outlines? Or is it something else entirely?

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Should be well explained here.

These two layers contain the reference marks for fiducials on your board. Never heard of these? They’re little marks placed on your PCB on the top and bottom layers that allow a pick and place machine to recognize where your board is located in physical space. At a bare minimum, we recommend including at least 2 reference marks on your design, but 3 is preferred by most manufacturers.

But you can (mis) use this layer as you wish given you mind information in it when (and if) exporting it to Gerber.

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