Restore production data flow

This issue is for tracking issues related to the effort of cleaning up loose ends that restrict refinebio from ingesting new experiments as well as generating a new compendium. This work will be mostly centered around fixing broken surveyor, downloader, and processor functionality. This collection of work will start after addressing project modernization.

Start by reviewing the project modernization work, since this effort is explicitly planned afterward. Then investigate the broken surveyor, downloader, and processor functionality; the work is done when refinebio can ingest new experiments and generate a new compendium.

Written by the indexing model from the issue text.