Port scripts to augur curate

[joverlee521]

To reduce the need to vendor ingest scripts and the need to document the vendoring process, I am prioritizing porting curation scripts in this repo into augur curate subcommands.

To prevent blockers, I am aiming to port over the scripts as is with the addition of tests in augur.

TODOs

• augur curate apply-geolocation-rules augur#1003
• augur curate apply-record-annotations augur#1482
• augur curate abbreviate-authors augur#1483
• augur curate rename augur#1484
• augur curate parse-genbank-location augur#1485
• augur curate transform-strain-name augur#1486
• Release new version of Augur with the new curate subcommands

Post clean-up

• Update repos using the vendored scripts to use the new augur curate commands. Listed individual issues below in order of importance:

  1. ingest: use new augur curate commands  pathogen-repo-guide#49
  2. ingest: use new augur curate commands zika#68
  3. ingest: use new augur curate commands mpox#262
  4. ingest: use new augur curate commands measles#44
  5. ingest: use new augur curate commands dengue#74
  6. ingest: use new augur curate commands seasonal-cov#26
  7. ingest: use new augur curate commands rsv#67
  8. ingest/ncbi: use new augur curate commands avian-flu#67
  9. ingest: use new augur curate commands yellow-fever#8
  10. ingest: use new augur curate commands rabies#1
  11. Update vendored scripts ncov-ingest#454
  12. ingest: Update vendored scripts forecasts-ncov#103
  13. ingest: use new augur curate commands hbv#15

• Update creating-an-ingest-workflow docs to new augur curate commands docs.nextstrain.org#212

• Remove scripts ported to augur curate #44

[joverlee521]

Closing this issue since we are done with porting scripts to augur curate.
There are still remaining pathogen repos that can be migrated, but they can be done in the future.