Best practices for Cygwin install on Terminal Server in app mode?

[Alex K. Angelopoulos]

I've tried installing Cygwin on a Win2003 server in application mode, and
see some problems with environment initialization just like reported with
the release candidates several weeks back.

This isn't a really common platform or deployment situation yet and I'm
only doing it as an investigation at present, so I plan to shift thinking
modes and run through setup on a Windows 2000 server with TS in App mode.
That should be the best baseline comparison.  Before I do, are there any
known "best practices" for TS shared installs of Cygwin?  Or will drafting
some be "my" job? ;)

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