I've been using cygwin buildbot for some time, doing pure windows
builds.  The trick is to have the cygwin buildslave unset a few environment
variables (like cygwin's PATH and TEMP and temp), then run a windows
batch file to do everything involving compilers, e.g. running
windows cmake.  There is a tiny bit of magic involved in cleansing
the environment enough for the windows tools to be happy,
but not much.

But I agree: for cmake and things like ninja that run compilers,
use pure windows versions, even if you kick them off originally from a
cygwin shell script.
- Dan
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