I've written an article on our Web site
in which I explain how to setup an Ant script bundling all the actions, from compiling your application to starting the execution on the EV3, including uploading the jar. I find it easier to use than clicking here and there for creating the jar, then copying it on the remote system (aka the EV3),... I'm not a big fan of endless clicking sessions
It works under Eclipse of course, but also directly from the command line.
Since it does not rely on any platform specific command (not even scp thanks to jSch lib and Ant extension), it should work fine on Windows, even without Cygwin installed. However I can't certify it 100% since I'm working with Linux boxes only.
Unfortunately (for you) the article is written in French, until I find some free time to put an English version online. Anyway, an Ant script is an Ant script, whichever language you speak
And Google translate may help a bit, although I've hard to understand the text it produces when asked to translate it in English
Don't hesitate to contact me if you need some explanations. Just click on my first name (Eric) on the article header and use the mail editor at the end of the bio and articles list page which is displayed then. You can also post a message in this board if you prefer, but I don't come here everyday.
Hope this helps.