Cobertura file not created despite out.json is

### Context
Hi,
I have instrumented the code using the following command:

```
npx nyc instrument --compact=false src instrumented
```

and to be practical I have moved the instrumented folder into `src` (esier) and I have committed everything into the following repository: https://github.com/fasatrix/nyc-test-folder-outside-src

Please install both `package.json`. The one in the root and the other within the `test` folder

To run the tests use `npm run cypress:run script`

### Current behavior:

Despite the `out.json` file has been create in `.nyc_output`, cobertura and other coverage types are being created empty

### Desired behavior:

Cobertura and other coverage types should be created

### Steps to reproduce: (app code and test code)

Just clone the repo, install dependencies, run the the app and the test

### Additional Notes

If I use the standard configuration and keep the "Cypress" folder at the same level as the `src` one everything works fine (repo for reference below). However for the project project I am working on (These are demos with the structure as the actual project which is confidential) I am unable to use this working configuration as I need to keep all test types(performance, e2e, cross browsers eyc.) within the `test` folder

https://github.com/fasatrix/nyc-test-folder-inside-src

### Versions

Win 10 Cypress 3.4