Refactor physics module

**Summary**:  
*  Modifies the Dynamical objects realted classes to generalize for any problem state. This allows for rigid bodies, deformable bodies using FEM and pbd under one dynamicalObject base class.
* Adds common interface for pbd solver and FE solvers to allow simpler code in SceneManager
* Refactors all the PBD classes for bugs, style, warnings and efficiency.
* Misc. modifications including rearranging folders, example codes, renaming classes and clearing some warnings.

See merge request !103