Full Migration to CollectOSS Naming

The initial renaming process for CollectOSS (PR #2) only renamed those references which could be changed consistently within the application itself. This was the majority of the references (docs, variables, etc).

However, some references remain in some external-facing places, including:

- [x] migrate environment variable naming prefixes and `auto_envvar_prefix` in CLI
- [x] migrate primary config file name (augur.json)
- [ ] migrate names of other config files (augur.db.json or whatever its called)
- [ ] rabbitmq default username and vhost settings (baked into the container as described in #278 )

These instances of the previous name have been held back so that the initial 1.0 release can be as drop-in as possible with existing docker-based (and relatively up to date) instances of Augur.

This issue is meant to track all these remaining references and assist in writing a thorough migration guide to allow instances to fully transition to CollectOSS.