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 suitable for deployment in an Eclipse product.
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:
Select File > Export... > Deployable plug-ins and fragments
Select the plug-ins and fragments you want to export.
The export destination can be an archive or a directory.
The recommended format for a deployable plug-in in 3.1 to be packaged as a JAR archive. Refer to the Exporting your plug-in as a JAR document for details if you have a pre-3.1 plug-in that you need to JAR.
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.