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I suggest to add new persistence type for TopComponent: PERSIST_ALWAYS_START_CLOSED (feel free to change this name). It should behave like PERSIST_ALWAYS (i.e. always remember where user docked the component) but don't show the component on IDE start. We need this for DLight indicators. There is no sense to show these indicators until the first C/C++ project is run from IDE. I believe other components would benefit from new persistence type as well, e.g. JUnit test results.
I think, NB has quite annoying usability problem due to absence of such mode. For instance, each time I reopen IDE I see nice Welcome Screen hidden by empty Output window, empty Search window, empty Find Usages window... There are no reasons for that tabs containers to reopen on IDE reopening, because they are always empty and only waste space.