Fine tuning the Nextclade all dataset

[j23414]

Description of proposed changes

When testing the dengue/all (serotype-level) dataset for accuracy, multiple people realized there was a trend of false-positive DENV4 classification. This PR mostly fixes that.

The dengue/all dataset was improved by:

1. Adding some "--penalty-gap-*" attributes to promote contiguous alignment (instead of gappy)
2. Adding a reconstructed root into the all tree.

This fix was inspired by multiple sources of feedback, and the mpox codebase.

Related issue(s)

• https://github.com/nextstrain/dengue/issues/21

Checklist

• [x] Checks pass
• [x] The serotype assignment should mostly match the NCBI GenBank annotations

[j23414]

Due to seeing similar issues with genotype-level datasets (e.g. denv4), I'm either going to either expand the scope of this PR to also fix DENV1-4 or split those out into separate PRs.

I'll start by adding outgroups/reconstructed ancestral sequences for each genotype-level dataset, perhaps as suggested by: https://github.com/nextstrain/nextclade_data/pull/203#issuecomment-2143765789

[j23414]

Incorporated edits and summarized said edits in https://github.com/nextstrain/nextclade_data/pull/203#issuecomment-2147990229 This is ready for review and dataset evaluation.

[j23414]

The genotype-level datasets require further improvement to meet the desired standards. However, the serotype-level dataset is functioning as expected.

To solidify the progress made with the serotype-level dataset, I move to merge the changes and shift the focus to enhancing the genotype-level datasets in a new PR.

This approach helps me avoid mixing completed tasks with those that still need refinement.