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Date: Thu, 14 Jan 2016 14:21:08 -0500
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> In pcb there should be an import footprint list or similar
> feature. In such case gsch2pcb or netlist would write down what
> footprints are used in design instead of importing changes. Then
> footprint listed are imported unlisted elements will be deleted and
> new elements added.

File->Import does that.  Any new footprints are added at to a
specified region, changed footprints are changed in-place, and removed
footprints are merely selected so you can see what they are before you
hit the delete key.

The import feature uses the same gnetlist (just a different backend)
as everything else, you can run it yourself to see what the file looks
like, or have other programs generate the same type of file.  It's not
magic.