In Eclipse 3.x you can remember the current application state (the user’s layout and window size) between application sessions, via the setting configurer.setSaveAndRestore(true); in the initialize method of ApplicationWorkbenchAdvisor. See Eclipse RCP Tips and Tricks for details.
But of course this is not true.
e4 has two command line options to get a similar behavior then in Eclipse 3.6. If you use the command line option “-clearPersistedState” then the user changes will be deleted.
I believe “-deltaRestore” is intended to work similar to setSaveAndRestore(true). Currently in Eclipse 4.1 M2 the state is always saved but I think that is a minor bug. See https://bugs.eclipse.org/bugs/show_bug.cgi?id=313883 for details.
Many thanks to Remy Suen for the tip on these parameters.
Once the bug discussion has been finished I will update my Eclipse 4.0 Tutorial.
[UPDATE: The parameter is not called deltaIgnore instead of "deltaRestore".]