ingest: remove .gz/.xz files and `date_submitted` column by TBD

[joverlee521]

Context

Follow up on #317:

In ~1 month, I'll remove the gz/xz file uploads and delete them from S3 so that we don't continue to upload duplicate files with different compressions.

Follow up on #319:

Preserving the date_submitted column for now to give users a chance to switch over to the new column. I plan to remove the date_submitted column by 28 July 2025.

TODO

By TBD

• Write blog post about changes in mpox nextstrain.org#1192
• remove gz/xz file uploads from nextstrain-automation's files_to_upload config - gz/xz files no longer updated as part of Ingest from Pathoplexus, adapt phylogenetic to use Pathoplexus accessions #342
• manually delete gz/xz files on S3
• revert bb47794 to remove the date_submitted column in metadata.tsv on S3 - column no longer exists as part of Ingest from Pathoplexus, adapt phylogenetic to use Pathoplexus accessions #342

[joverlee521]

And of course I missed my own deadline...Pushing this back a bit to announce the changes more widely.

[joverlee521]

Upstream data source was changed to PPX in #342.
As part of this change, gz/xz files are no longer updated and the date_submitted column has been removed.

[joverlee521]

Based on the forked NW-PaGe/mpox, the WA DOH folks are still using the gz/xz files, so I've notified them on Slack about switching from gz/xz files to zst files.