Sure I have all that. But I did the build from a non-Posix shell (hate bash).

Yes, I understood. But when you run sh you very likely execute your Cygwin shell [1] and the custom command is executed by that (Posix) shell, presumably bash. The scripts run by that shell don't use Windows commands, they are using Posix shell commands. What I wanted to say is that in your environment the minimal patch you provided works because it executes your Cygwin shell and all commands within that script are run in your Cygwin environment whereas a bare Windows environment wouldn't be able to use cp and many of the other commands in these scripts.

That said, your patch may be fine for your environment but unfortunately not for other Windows users in general.

I thought something like: ... [CMake code above] ... would do it. But then again, I'm a n00b when it comes to Cmake.

Your CMake code doesn't look bad (thanks for providing it) but it would only solve the issue if sh was a valid Windows command and ran a Posix shell that could execute the make_header script and others.

Note: I tried to build the pdf docs under MSYS2/MinGW-w64 on my Windows test system yesterday (for comparison) but this didn't work out and I ran out of time. Something was missing from the latex installation. I'll continue later when I have more time to investigate this issue.

[1] This requires that your Cygwin environment has been added to your Windows system PATH which I do not recommend, BTW, because it may obfuscate what's going on: your Windows shell inherits some commands like cp from your Cygwin (bash) environment etc..

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