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Native Windows Support vs Cygwin

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I'm writing a hacking utility (see http://forums.hak5.org/index.php?/topic/27053-aircrack-ngui-graphical-interface-to-aircrack-ng-dsniff-nmap-and-more/) and am running into a question of choice. I'm trying to add Windows support to the app so Windows and Linux users can experience the hacking goodness. The problem is that (almost) every program I invoke on the already-developed Linux end needs to have a Windows equivalent to work properly. This could take a large amount of time and result in two forms per feature, one for Linux and one for Windows. My (somewhat) solution would be to make Cygwin a requirement for Windows systems so I can continue to use my Linux syntax in a Windows system. Problem with this is that a terminal window will always be open (to send my Linux commands to) and parsing could be a little bit more difficult, but not as difficult as multiple forms.

So, my question boils down to that of programming experience: should I have my app do native Windows calls to get and set the information it needs, or should I use an emulating suite like Cygwin so I can keep my existing Linux commands at a price?

>inb4 "Why Windows?" - My app isn't getting as much traction as I'd like, so I think supporting Windows might generate more interest.

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