refactor(models): add default value for outputDir

[BioPhoton]

I tried to reduce the scope as much as possible. In addition I added comments in code and here to understand the changes better and have and easier review process. Hopefully this makes up the messy change.

This PR includes:

• refine options
  • tests
  • separate functions for upload and persist
• model changes
• tests
• refactored options, config and defaults
• moved filename into defaults in config middle ware
  (formats follow in fix(cli): fix json format handling #360 )

Resources:
Overview of the target architecture can be found here: https://github.com/code-pushup/cli/wiki/Research:-Module-architecture-and-responsibilities

closes #321

[matejchalk]

Thanks for the explanations. The persist config handling now looks good 👍 But the same strategy cannot apply to the upload config, as described in comments.