You can't connect to native applications like that with Flex or AIR.
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Not 'directly' anyway... there is always the option of running a socket server that will take commands from your Flash/Flex/AIR app to do those kinds of things. You could also use a web server, web services, or a servlet to accomplish the task (read: security needs some thought).
Then... there is always Merapi (I love Merapi) which requires some Java chops.