For my "cygrun.exe" wrapper to work it should be behind shebang scripts in the PATH, so moved ~/usr/bin to the PATH end on Cygwin.
QUILT_DIFF_ARGS="--color=auto -p ab"
QUILT_DIFF_OPTS="-p"
QUILT_REFRESH_ARGS="-p ab"
QUILT_PUSH_ARGS="--color=auto"
QUILT_SERIES_ARGS="--color=auto"
QUILT_PATCH_OPTS="--unified"
QUILT_NO_DIFF_INDEX=1
QUILT_NO_DIFF_TIMESTAMPS=1