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One can specify references to external jars in the <RUNTIME> section of the plugin.xml files. However, these references do not appear to be added to the classpath when the plug-in is launched inside PDE (by run in runtime workbench option). In most of the examples and supplied plugins, these references only ever appear to be references to other plugins. However, if your plugin is dependent on other code, you will often want to reference jars that are not plugins. I suspect that this problem can be fixed easily when you deploy the plugin because you can simply stick the referenced jars in the plugin's folder but that doesn't help at development time - you want to use the run in runtime workbench option.
Moving to Platform Core for investigation on plugin parsing. If it works in a "normal conditions", we should move it to PDE to investigate if it is a problem in "runtime workbench".
*** This bug has been marked as a duplicate of 3074 ***