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When you choose to import all of Eclipse with source the JavaIndexing thread will take 204,248 ms (about 3 1/2 minutes) with auto build off. With auto build on it takes 511,958 ms (about 8 1/2 minutes) - perhaps turning it off for the duration of the import and then doing a bebuild all afterwards might help.
WorkspaceModelManager spends 6990 ms processing resource changes regardless most of that is in createWortkspacePluginModel (4786 ms).
Moving to PDE/UI for comment.
PDE needs some time to digest all the plug-ins (parsing the manifests and building the models). This time has been significantly reduced in the default case because the models are loaded directly from the live registry (no parsing is involved). This covers majority of the cases. The rest (targeting another Eclipse application) will still have a parsing hit but due to a less frequent usage is not considered critical.