many changes for pi compatibility

* changed colouring for better visbility
* code refactored for more modular structure
* phase wrt to PEMs now included in reconstruction, angles between -90
and +90 degrees
* arbitrary box config possible, up to 10 boxes, from MSE or MER
* upshift option to move Pi result into Sigma result for comparison
* automatic RzA calculations from MSX shotfile information and FARO file
* incompatible time points highlighted in plot