* Update template files to remove instructions and placeholders
* Add Genbank and GFF references
* Bring in phylo workflow from pathogen-repo-guide and modify to work

Also remove exclusion from .pre-commit-config.yaml

* Drop to Python 3.11 in GitHub pre-commit CI, to match actual
  development practice
* Clean up formatting of several files
* Convert all Markdown links to use reference dictionary at end of
  file
* Add `log` and `benchmark` to all Snakemake rules that didn't have
  them
* Remove `dump_ncbi_dataset_report` rule

Also adds logging redirects everywhere

subrepo:
  subdir:   "ingest/vendored"
  merged:   "980c010"
upstream:
  origin:   "https://github.com/nextstrain/ingest"
  branch:   "main"
  commit:   "258ab8c"
git-subrepo:
  version:  "0.4.7"
  origin:   "https://github.com/ingydotnet/git-subrepo/"
  commit:   "c9ec2a6"

* Switch Auspice to default color-by=region
* Remove extra `metadata_columns` (and associated config) when calling
  `augur export v2`
* Move `--columns` arg of `augur traits` into config
* Add `--metadata-id-columns` arg to `augur traits` invocation --
  fixes issue where traits were being improperly inferred
* Use a mid-point tree rooting