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Don't cleanup the dead nodes when pruning the tree

Ondřej Surý requested to merge 3646-use-after-free-triggers-a-crash-in-reactivate_node into main

The dead nodes might get reactivated during the db iterator walks the version of the tree, so we can't cleanup the dead nodes while the db version is open. Restore the previous behaviour that cleaned up the dead nodes when we are closing the version.

Closes #3646 (closed)

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