Move s3_dst config to top level config

[j23414]

Description of proposed changes

Nested configs for s3 URLs are challenging to override by the Snakemake --config option, as discussed in the following comment:

https://github.com/nextstrain/dengue/pull/13#discussion_r1361131210

This moves the url to the top level as a s3_dst config value, and propagate those changes to the relevant Snakefiles. It's important to note that I haven't conducted thorough testing, and there may be nuances in the implementation meant by the comment. Suggestions or clarification welcome.

Additionally, I was unsure regarding whether the s3_dst config should be a required value or an optional default (Snakemake styleguide: config values).

Related issue(s)

• https://github.com/nextstrain/dengue/pull/13#discussion_r1361131210

Checklist

• [ ] Checks pass

[j23414]

Since we can use: --config upload='{"s3": {"dst": "NEW URL"}}'

https://github.com/nextstrain/dengue/pull/13#discussion_r1375081279

This PR is no longer necessary.