Database code cleanup/architecture

[john-science]

We currently have these two files, that contain four classes:

• database.py
  • class Database
• database3.py
  • class Database3(Database)
  • class DatabaseInterface
  • class DatabaseLayout

I like base classes, but no one is using the Database here, so I think it should just go. Also, the three classes in database3.py should be each in their own file.

Also, the unit tests for each are in crazy places right now.

The only trick here will be to make sure that any external imports still work, so make sure that database3.py still imports all the classes it used to have (plus some pylint disables, so people don't remove the unused imports).