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I missed this the first time around. What you need is a small sed script in your postinstall script. The sed script can replace some symbol with the output from 'cygpath -w /usr/X11/....'. As for linefeed issues, AFAIK windows will process bat files with unix format, but you could always use d2u in your script. Additionally you need to make your package depend on the tools you use in your script.
Too late ;) http://cygwin.com/ml/cygwin-xfree/2002-07/msg00318.html but thanks anyway Jehan
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