Suggestion for the Cygwin developers: What about a file in /etc that contains contain environmental variables that sets cygwin-specific variables and overrides anything in Windows' environment?
It would also make it possible to clone an installation by copying - no need to modify the environment. See https://cygwin.com/ml/cygwin/2010-01/msg00977.html Sorry, I'm not a coder and cannot contribute a developer a cannot propose a path. As previously: "Just a suggestion, not a request." Best wishes, - Barry Disclaimer: Statements made herein are not made on behalf of NIAID.