> So can "command proxy" execute something I talk above? Yes it can, because it has full access to the desktop (within user permissions). I'm not sure if Java has the ability to use ActiveX objects, but I believe it does. There is a .NET command proxy concept out there too, but it isn't as developed/advanced as the Java one.
> But if I create web > app, and run in IE (I accept the app only run in Windows, with Office > is installed) can the app has upload ability? Yes, as long as the server you are uploading to has a crossdomain.xml file that allows access. Personally, given you have accepted the constraints of Windows only, and are willing to have a desktop app, I'd take a look at creating a Java/.NET app instead if you have the skills available there. It would be a lot easier and have access to ActiveX, and with WPF, you even get the cool UI stuff that Flex/Flash has. Both Java and .NET apps have the ability to launch from the browser too - Java Web Start and ClickOnce respectively. Silverlight won't help here btw, only full blown WPF apps will.