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Hello Sebastian,
the most direct way for adding support for iAlertU would be the
author of iAlertU adding support for Remote Buddy. It definately
won't work the other way round, since I have not done any research on
ways to emulate the Apple Remote for other applications. But it is
likely, there is no way to do this anyway.
For now, please write an email to the author of iAlertU, if you need
this functionality. I'll likely write one myself lateron, but I'm
pretty busy with getting some changes to the foundation finished.
Felix