Tidy and improvements of ComputeAlignment.py

In ComputeAlignment.py:
- plots are now saved for post-alignment cross checks
- added pauses at important points to allow user to consider plots
and continue or stop
- removed old test code

In ToolBox.py:
- removed obsolete TrackClusterCorrelation_Test
- PerformPreAlignement now returns plots for saving
- added checks in Perform3StepAlignment that the optimisation actually
converges, asks user what to do if not