Documentation update before the fault tree structure change.
Intermediate events to gates change in Supersets.
Gates and Nodes instead of events in a fault tree.
Rename files after introducing node classes.
Introduce FaultTreeAnalysis instead of FaultTree.

This should have been done from the start because FTA implements
RiskAnalysis not FaultTree. Fault Tree should be a tree that is used in
FTA.
Add Fault Tree Class representing the tree.
XML input file for TwoTrain fault tree.
XML input files for ABC and AB_BC fault trees.
Add fault tree pointer in fault tree analysis.
Node to event change and Basic/House event separate classes.
New input xml files.
Deprecate Transfer symbols as gates behavior.

This is done because the new XML input format has a include directive
with a different behavior. The transfer symbols will be used to
indicate re-used gates in future.
Simplification of fault tree class before putting into analysis.
Adding nodes to the fault tree through analysis initialization.
Use boost dynamic casting to determine primary events.
Better naming for private functions of FaultTree class.
Adds xml parser tests from Cyclus Project.
Test callings of fault tree functions in analysis.
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.