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Old autoupdate was running in non-modal mode and as such when one was downloading big NBM files, one could switch to editor and do various more useful tasks than watch the download progress. This does not seem to be possible anymore and seems like a pretty uncomfortable regression to me.
This is really visible now, when tomcat is not part of the base ZIP and I have to always download it once again from the AU center.
It is not a part of current UI spec. nor subject of proposed UI change, until UI spec. supports not-modal state it won't be implemented.