Compiling the Atari ST core for the MIST is pretty straight forward like described here. For the minimig core some prerequisites are needed which I’ll describe below.
The amiga_boot.v file is missing and needs to be compiled before using the Altera Web Edition to compile the core.
I was lazy and took the mingw build environment used for XBMC (https://github.com/xbmc/xbmc/tree/master/project/BuildDependencies). I used it to compile vasm which is needed to compile amiga_boot.

1. Get the sources from here: http://sun.hasenbraten.de/vasm
2. Unzip it to vasm
3. Go into vasm and type
   make CPU=m68k SYNTAX=mot

I copied the binary vasm68k_mot.exe to a bin directory in the mingw env. Since the xxd binary was missing as well I download the msys-vim package from sourceforge and installed it in the mingw env as well.
When I got some time I’ll create a stripped down mingw/msys env with the binaries needed to compile the firmware and amiga_boot.
Once done we need python for windows in path. With some smaller changes to the python scripts and the makefile I was able to compile the amiga_boot files. Once finished I’ll submit the changes to the MIST main repo.
Meanwhile you can use the files from here: https://github.com/wsoltys/mist-board/tree/master/cores/minimig/fw/amiga_boot/bin

Copy those files to the same directory structure of the MIST main repo clone and open minimig_mist.qpf with the Altera Web Edition. In the Web Edition you need to enable talkback in order to use the Signaltap which is needed to compile the minimig core.

1. Go to Options
2. Internet Connectivity
3. Talkback options and enable them

Now you can start the compilation and after some minutes its done 🙂