Various fixes for the phylogenetic workflow automation

[j23414]

Description of proposed changes

This pull request addresses several issues that emerged after implementing automation for the ingest and phylogenetic workflows. The following improvements have been made:

1. Renamed the final phylogenetic dataset from WNV-nextstrain_NA.json to WNV.json to align with the automation's expected format (<pathogen>.json or <pathogen>_*.json).
2. Removed outdated output files from the phylogenetic/auspice/*.json directory to streamline the repository.
3. To the phylogenetic workflow, added rules to download metadata and sequence files from s3 instead of pulling from the ingest/results directory
4. Resolved an issue where uncompressed versions of metadata and sequence files were being uploaded due to the use of outdated scripts/upload-to-s3 scripts.
5. Fixed the above bug by git subrepo-ing the vendored scripts and using the fixed vendored/upload-to-s3 script
6. Delete any remaining unused or redundent scripts from the ingest/scripts folder

Related issue(s)

• Originally wanted to address issue: Change the final auspice dataset name #17
• Ended up needing to address issue: Use vendored scripts instead of maintaining a separate copy #15
• Partially addressed issue: Refactor phylogenetic workflow to allow either ingest/results/locally_annotated_data or download open data from s3 #18

Checklist

• Checks pass