From the (included) Readme:

These are the tools we use to make automaps in thief. Here's the basic process

1) make a file P001ra.pcx that is the automap page one with *all* the annotations
2) Draw bounding boxes around the annotations in color 254
3) From a DOS box, run "cutout p001ra.pcx" to generate the p001rXXX.pcx files
4) Run "makerect p001ra.pcx" to generate the p001ra.bin file

If you have annotations that overlap, you can spread them over multiple files, just feed all the files into both tools on the command line in the same order (e.g. "makerect p001ra.pcx p001rb.pcx" etc).

If you have problems getting these to work, let me know. Though, like all of dromed, they are unsupported. - MAHK (emailadress see readme file)

Here's an automap creation tutorial.

I wonder where I got this tool from because it seems to me now that this will only work for thief. And their maps are quite different than the SS2 maps. Maybe someone with some dromed/shocked experience can tell us more about this.

Just to confirm, this definitely does work for making SS2 automaps. The process is slightly different from the Thief method, hence its better to use the new tutorial. Shame the tut pics got lost though.