During the 3.0.x upgrade Crucible attempts to remove duplicated stored paths from the database. Apparently the deduplication task breaks if there are any unprocessed cru_feindex_msg rows. Those tasks are usually consumed on every incremental scan of the repository, unless pulling was disabled.

Fix would require changes to the deduplication script to handle this case.

As a workaround user may want to run old instance one more time, ensure all repositories are scanned incrementally (either via automated pulling or via manual incremental run triggered from administration/repositories/repository page)