Convert a Photoshop Batch process to GIMP or ImageMagick process that can be scripted from a command line

We presently have a Photoshop Batch process which modifies a set of images to produce a set of output images. We need to be able to automatically run this process from a command line, however the Photoshop Batch process cannot be run from the command line (it requires a user to start it off). Assume that we need to run this process as a Windows Scheduled task, or from Linux under CRON (either Windows or Linux scripted solution both acceptable). The steps must be *exactly* the same as the Photoshop steps, so that the outcome is consistent with existing. there must NOT be any human interaction required, this process needs to be completely automatci. Please review the attached image showing the sequence of commands that needs to be altered. Note that there are some 'polygon' selections that need to be matched identically, you will need to get these masks out of Sherlock