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Eclipse F2 If you try to add PlugIn Dependencies to another project, installed PlugIns arn't available any more. This occours with a fresh Eclipse F2 installation with an newly created workspace. It doesn't occour on an updated F1->F2 installation. Steps to repeat: create a new Plugin project, open plugin.xml->Dependencies klick "Add", only "Workspace Plug-ins" are shown not "External Plug-ins".
Go to PDE preferences - Target Platform and check if external plug-ins are disabled. If they are, the wizard is correct - it cannot allow you to add dependencies to plug-ins that are not visible (being disabled).
You're right. But you should collect these changes in one place to avoid these unnecessary bug entries. Last time I installed F1 the behavior was contrarily. All Plugins where selected by default.