When output is set in config file, the path is wrong in ts.config.json

When we define an output in command line like

```bash
missdev --output=libs
```

then the path is the right one in tsconfig.json. But when we set the output directly in `mrs.developer.json`, the path in tsconfig.json is the default one.

Reproduce the difference between `missdev --output=libs` and an `output` value in `mrs.developer.json`, then inspect the configuration handling and the code that writes `tsconfig.json`. Compare the generated paths in both cases; done means the config-file path matches the command-line path instead of falling back to the default.

Written by the indexing model from the issue text.