Fix extract to build index for dataset after move using new config

[Aaron09]

Without an index built during extraction, it would attempt to be built during the gitlab pipeline submissions, but those don't have write access to the '/data' filesystem and it fails. Index must be created off of new config during extraction. Since the new config and old config formats are different, we cannot just move the already built index for annotations.

This shouldn't be an issue to do once extraction is handled asynchronously from the user.