Hi Dan,
I've just visited the pure-data repo on github and it seems like your auto-tools branch is now merged in. I cloned the repo and I could compile without errors (last time I got stuck in the extra folder, if you remember) but the only files in the bin folder are:
pd.exe, pd-gui, pdreceive.exe and pdsend.exe.
So I'm missing some files, most notably pd.dll and wish85.exe. Any ideas? Not that it's urgent, just wanted to point it out. I'm on Windows 7 + msys2 and I'm always happy to test stuff.
Christof