Update repo structure to match pathogen-repo-guide

[joverlee521]

User in office hours was confused by the structure and directories in this repo. It would be easier to explain if the structure matched the pathogen-repo-guide and we could point them to related documentation.

TODOs

• Add detailed usage docs #44
• add top level nextstrain-pathogen.yaml
• move top level workflow to a phylogenetic directory
• update rebuild workflow to use phylogenetic directory
• add phylogenetic/build-configs/ci (could probably resolve CI workflow runs are ~10 mins #69)
• update CI workflow to pathogen-repo-ci.yaml@master
• update rsv pathogen-repo-ci in other repos (augur, docker-base, conda-base)