It is possible to alter the list of plug-ins and fragments that PDE will pass to the run-time workbench when running or debugging.
By default, the Plug-ins tab is configured to select all the workspace plug-ins and external plug-ins that are enabled in the Preferences.
You also have the option to launch with any subset of those plug-ins. This gives you great flexibility, but with flexibility comes the danger of ending up with an invalid configuration. Use this feature carefully and press Add Required Plug-ins to ensure the subset is complete.