Here is the command line. Given the list of images (im1.xxx, im2.xxx etc, im1 being the bottom layer,) a list of labels for the layers ("label1", "label2"...) :
convert ( -page +0+0 -label "label1" im1.xxx[0] -background none -mosaic -set colorspace RGB ) ( -page +0+0 -label "label2" "im2.xxx"[0] -background none -mosaic -set colorspace RGB ) ( -clone 0--1 -background none -mosaic ) -alpha Off -reverse "out.psd"

That is, for each layer, you have something like
( -page +0+0 -label "optional_label" im1.xxx[0] -background none -mosaic -set colorspace RGB )

The label/name of the layer is optional (remove -label if none.) The [0] in im1.xxx[0] retrieves the first image in the image file, in case there exist a thumbnail in the Exif.