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I have tried updating
/home/<user>/.bashrc
/home/<user>/.bash_profile
/home/<user>/.profile
/etc/profile
/etc/bash.bashrc
And none of them are reflected in the log output. I'm unable to determine how Jenkins is getting the env vars once it is able to SSH into my Cygwin Windows machine. If I knew what environment file it was reading, I could perhaps work around this.