You don't need Flash CS3 to use AIR. As always, Flex is free.
In order to communicate to a program capable of manipulating files, you need either a wrapper (a program to embed the Player like for example a browser does) or to convert your app to a projector and call a program from that.
To do the first, you use either AIR or haXe's SWHX or some other shareware shit. They're both extremely simple.
To do the second, you have to be gay. Just make a separate program to do the file manipulation.
What language to use? Any fucking language ever. Unless you're on Windows your computer should already have a dozen compilers, otherwise download a C one of a few megabytes.