Describe subtree setup

The previous merge commit and its attached commits were created by the
following command:

    git subtree add --prefix ingest/vendored https://github.com/nextstrain/ingest HEAD

Add a section in the README on how to use this directory in the future.

README.md

@@ -27,6 +27,19 @@ snakemake --cores 4 -npf ingest/results/aligned.fasta ingest/results/sequences.f
 Ingest will fetch genomes from NCBI's Entrez API and write to `./ingest/data/genbank.gb`.
 As of mid 2023 there are around ~11k genomes and the full GenBank file is ~150Mb.
 
+### `ingest/vendored`
+
+This repository uses `git subtree` to manage copies of ingest scripts in `ingest/vendored`, from [nextstrain/ingest](https://github.com/nextstrain/ingest). To pull new changes from the central ingest repository, run:
+
+```sh
+git subtree pull --prefix ingest/vendored https://github.com/nextstrain/ingest HEAD
+```
+
+Changes should not be pushed using `git subtree push`.
+
+1. For pathogen-specific changes, make them in this repository via a pull request.
+2. For pathogen-agnostic changes, make them on [nextstrain/ingest](https://github.com/nextstrain/ingest) via pull request there, then use `git subtree pull` to add those changes to this repository.
+
 ## Phylo
 
 * For a small ~500-tip dev tree: `snakemake --cores 4 -pf auspice/hbv_dev.json`