Full Migration to CollectOSS Naming

[MoralCode]

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:

• migrate environment variable naming prefixes and auto_envvar_prefix in CLI
• 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 Stop building config files into the rabbitmq image #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.

[MoralCode]

Migration guide notes so far (do not follow these until they are put in the migration guide in the repo wiki, they might be wrong here):

• docker networking: up to the admin - as long as all the containers are together it doesnt matter