Added event skip to ComputeAlignment.py, so alignment considers whole run.

In ComputeAlignment.py:
- defined a skip to ensure that 10000 events from the requested total are considered
- strongly recommended that the total considered is -1 (all events)
- changed how the name of the alignment file is defined, it now contains the parameters
used to create it
- changed default gtol from 1e-3 to 1e-5
- improved help text
- tried to replace alignement with alignment everywhere

In ToolBox.py:
- tried to tidy up comments in functions used for alignment procedure