Although I am not sure that I fully understand your questions, I am afraid that it is not possible to convert a CloverETL project to a JAR file. You can run each part of the project (e.g. graph or jobflow) separately within the CloverETL Designer or you can convert it to a Server project and run each graph from there (you have also more options within the Server like request URL or wget command).
As for your second question, in Eclipse you can open a project in CloverETL perspective (Window -> Perspective -> Open Perspective). You can then use CloverETL components from a Pallete and when your graph is ready, you can execute it using one of the options described in a documentation:http://doc.cloveretl.com/documentation/ ... raphs.html
Hope this helps. Best Regards,