Refactoring of simulation profiler

* Added call sequences and sparse profiling at each time step in
  SimulationProfiler
* Removed singleton in SimulationProfiler, now instantiated only in 
  ModelInstance class
* Removed deprecated SimProfileWriter class, Profile writing is now
  included in SimulationProfiler class  
* Added coupling tests functions and datasets
* Updated config.hpp file construction for log file names
* Removed IOListener dependency from Engine class
* Updated and Cleaned source code

(closes #38)