I was looking at the command line options for the ARM_Programmer.exe utility and noticed there is no option to specify the programmer. You can specify a programmer in GUI via the drop down.
It's potentially important because I have 'gang of four' situation, programming 4 boards at a time.
Also was looking into building the code via msys. I'm assuming everything is built under msys? x Except the documentation? Related to that I noticed on the web page you say
Run the command CollectExternalFiles. This appears commented out. Should I use Collect Shared files instead?