Update documentation

[jwhitlock]

Update the deployment documentation:

• Recreate the deployment diagram. I do not have access to the original diagram, so I recreated a much simpler version, omitting some of the details.
• Refresh the text
• Mention monitoring the replica lag and database disk usage
• Update the instructions for current versions of the docker images
• Include creating a test API key

Other changes:

• Fix the auto-documenting environment configuration
• Mention the innodb_log_file_size fix.

Fixes #1385.

[jwhitlock]

User @HJJac wrote a script at #1642 (comment) that was very useful in updating these documents, and may be useful if you are trying to run Ichnaea via the Docker images. I decided against adding a script to the repo, because of the maintenance burden, and because local development is much easier with Docker and docker-compose.