Move phylogenetic workflow from top-level to phylogenetic directory
to follow the [Pathogen Repo Guide](https://github.com/nextstrain/pathogen-repo-guide/tree/main)

Part of work to update this repo to match the pathogen-repo-guide.

Part of work to update this repo to match the pathogen-repo-guide.

Part of work to update this repo to match the pathogen-repo-guide.

Part of work to update this repo to match the pathogen-repo-guide.

Following the pathogen-repo-guide and
nextstrain/zika@efe11e3

Update top-level and phylogenetic `README.md` files to
match new workflow structure that includes ingest and
phylogenetic directories, following the pathogen-repo-guide

Add empty top-level `nextstrain-pathogen.yaml`
to allow `nextstrain build` to work from any
directory regardless of runtime, as described [here](nextstrain/pathogen-repo-guide@e318589)