Codeintel xrepo data is not updated properly

Created by: efritz

We currently do not support two dumps providing a package, although this is an obvious scenario. We also do not update the lsif_pacakge/lsif_references table on conflict, meaning that if we upload another dump (or re-upload/retry the same dump for processing) that provides the same packages, we won't update the lsif_packages table and we'll delete the old dump, which cascades the package data with it.

This can be seen by uploading a dump, then re-uploading it. Every even-numbered upload will clear the relevant data in the table.