Real men port; wimps reinvent the wheel.
At work we have an extensive JNI layer for our Java applications to work with a series of cooperating Windows/Linux processes which implement our own file system and support services (remote printing, user/group management, etc). Sadly, we do not use Cygwin and are saddled with extensive #ifdef/#else/#endif code based on platform. (It also does not help that Windows was our first target platform.)
elliotth's outstanding Terminator program using Java/JNI/Cygwin would have been a good model for us in many respects had it been known earlier. It's a well thought out design and a beautiful application.
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