First go at removing Run2 specific code
This MR is the driver behind
- Lbcom!376 (merged)
- Analysis!547 (merged)
- Alignment!100 (merged)
- Stripping!1333 (merged)
- Moore!258 (merged)
- Panoramix!55 (merged)
- Castelao!53 (merged)
For some of the motivation behind this cleanup see