Fix a bug with forgotten re-use of a primary event.

The bug was that the re-use of a primary event was not detected.
Instead, primary events were reinitialized every time they were
encountered. This lead that a primary event had always one parent even
with re-use with another parent.
Documentation of the code structure and XML tools.
Risk Analysis is being separated.
Refactoring input analysis from FaultTreeAnalysis.
Input formatting tests are depreciated.
Remove unnecessary top_event for Risk Analysis.

Everything is either gate or primary event.