Restructure variant analysis manager tests

This restructures the variant analysis manager tests to follow this
pattern:
- Class
  - Method
    - Context
      - Context
        - ...
          - Test

Before, we were only using this pattern for some of the tests and this
made it confusing were which method was being tested.

By splitting this off, it will also be easier to move some of these
tests out of the cli-integration tests and into the no-workspace or
minimal-workspace tests.

Author: koesie10