Clean up and fix issues

- Got rid of the non necessary older tests (only displaying raw data without simulation)
- Reorganize the include/using lists
- Clean up the code to not have levels anymore, we know how many cubes/nodes we need.
- Proper physical parameter (from paper and material property)
- Reorganize the system build process and resolution (more simple and direct)
- m_name is a duplicate, a Representation already have such data member
- No need to store the number of boundary conditions or displacements, the vector structure should give us that information
 => changed the way we store these 2 (per boundary condition, instead of per dof)
- Got rid of the vector< vector< vector<Vector3d>>> m_nodes, the 3d positions should be stored in the internal state. No need to create additional data structure.
- Reorganized the test structure to add easily components to it (more flexible)
- Clarify the tests setup
- Rotate the truth cube data +PI/2 around X right on load
- Cube corners defined around the center of the truth cube data to avoid manual adjustment
- Truth cube initial internal nodes adjusted to match the uncompressed truth cube data set (if no load is applied, the simulated truth cube should match exactly the uncompressed data set)
- Add a simple quick error analyzer (display maximum error in meter across all beads)
- cpplint
- doxygen