Fixed Bin Edges and minor changes

2 minor additions to the project:
1. Ability to specify fixed bin edges in the control file.
The entry in the control file is as follows:
bins = 2;
binEdges = {-1.0, 0.1, 1.0};

The size of binEdges has to be bins+1 and must be in ascending order. For now the bottom and top limits are not used, they are the same as -inf and inf. If binEdges exists in the control file it replaces the current method of estimating the bin edges based on the minimum and maximum of the distribution.

2. Modified Rakefile to add the SimKernel as an include -I to avoid the use of so many relative paths in all the other files. Now the only relative path associated to the SimKernel should be in the Rakefile.