During the design phase, plug-ins and fragments in your workspace are used as-is so that you can quickly test and debug. Once you reach the stage where you are satisfied with your code, you need to publish it in a form fit for delivery on the platform.
The easiest way to do so is through the Export Plug-ins and Fragments Wizard. It shields you from ant scripts and does not pollute your workspace with resources generated during the build operations:
You also have the option to save the settings of this export operation. This way you would be able to redo this export operation without having to go through the wizard all over again.
Alternatively, plug-in JARs could be built manually. Refer to the Creating Ant Scripts from PDE section.