Harmonize with pathogen repo guide

[j23414]

Description of proposed changes

Harmonize the ingest code organization with the pathogen repo guide

Related issue(s)

• https://github.com/nextstrain/zika/issues/29

Checklist

• [x] Checks pass

• [x] post merge update of data.nextstrain.org zika files

• [x] Rename transform.smk to curate.smk

• [x] Simplify field name remapping

• [x] location of usvi data files

• [x] Harmonize the ingest/config/defaults.yaml file

[j23414]

As part of addressing this comment, I updated ingest but forgot to update phylogentic. Fixed in https://github.com/nextstrain/zika/pull/31/commits/b6d3ccbc1e60556bee39daa3e90ddb4239d0578b

[joverlee521]

Thanks for following up and addressing changes to match the pathogen-repo guide!

I've made a couple more issues to track some remaining tasks:

• https://github.com/nextstrain/zika/issues/32
• https://github.com/nextstrain/zika/issues/33
• https://github.com/nextstrain/zika/issues/34