Refactor runner.py

**🚀 Feature**

Refactor runner.py into smaller, easy-to-read functions.

**Motivation**

Current code is very difficult to read, contains too many nested layers, complex multi-line comments and confusing naming conventions.



[AB#7546](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/7546)