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First, you need to know that your plugin will *run* either way, although Eclipse folks claim that performance might differ (surprisingly, JAR-ed plugins are supposed to be better =>
http://www.eclipsezone.com/eclipse/forums/m91980917.html#91980917).
If that's all you want to doyour plugin is intended for, the choice is seems to be entirely up to you.
However, some plugins are intended to can be used by other plugins; such plugins expose packages to the clients. You must create a JAR file for a plugin that exposes packages, so that Eclipse's Plug-in Development Environment can locate the exported classes.
Note: if your plugin uses an external library, put it into edu.stanford.slac.external plugin and make that plugin required by your plugin.
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