This is a copy of the ingest directory from the mpox repo:

https://github.com/nextstrain/mpox/tree/c9b8282e2d56056c8b3c45fa860d931b320acd63

However, `ingest/vendored` subdirectory is not copied over since that folder should be
added with `git subtree`.

https://github.com/nextstrain/mpox/tree/c9b8282e2d56056c8b3c45fa860d931b320acd63/ingest/vendored#ingest

Future commits will change this to work with Dengue data.

…/vendored

subrepo:
  subdir:   "ingest/vendored"
  merged:   "a0faef5"
upstream:
  origin:   "https://github.com/nextstrain/ingest"
  branch:   "main"
  commit:   "a0faef5"
git-subrepo:
  version:  "0.4.6"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "110b9eb"

Temporary removal of Nextclade-related rules, pending the compilation of
a Nextclade dengue dataset and potential v3 changes.

May be added back in later.

Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>

Originally the field map was created to keep mpox NDJSON backward compatible
with field names used from NCBI Virus. However, this constraint is not
applicable to dengue.¹

This commit organizes field renaming into two parts.

1. Rename the NCBI output columns to match the NCBI mnemonics²
   (see "ncbi_field_map:" in `config/config.yaml`)
2. Where necessary, rename the NCBI mnemonics to match Nextstrain expected column names³
   (see "transform: fieldmap:" in `config/config.yaml`)

¹ #13 (comment)
² https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/#fields
³ https://docs.nextstrain.org/projects/ncov/en/latest/reference/metadata-fields.html