Refactor/improve project template structure

[rszamszur]

• I have searched the issues of this repo and believe that this is not a duplicate.

Feature Request

Small refactor for generated project from the template:

1. Technically JSON Responses (pydantic models) are Views in MVC, and should be kept accordingly to avoid confusion.
2. IMHO, .app.controllers.api.v1 submodule nesting is a bit excessive. Either .app.controllers or .app.controllers.v1 will be enough.

[rszamszur]

Changed coociecutter options:

• removed --skip-vagrantfile
• removed --skip-codecov