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Upgrade step for cleaning refences + detect and fix duplicates

Kirill requested to merge github/fork/cproensa/upgrade_clean_refences into master

Created by: cproensa

Adding the clean up step for config upgrade.

Also: Regarding avoiding duplicated references, this is my approach after discussion in https://www.mantisbt.org/bugs/view.php?id=21850 Note that the duplicated references scenario can also happen when bugs are deleted externally, bypassing the delete event. The approach here: first cleans up the duplicates, and then insert the correct one for the current bug.

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